Light-dependent Assimilation of Nitrite by Isolated Pea Chloroplasts

Chloroplasts were prepared from peas (Pisum sativum) in glucose-phosphate medium. In the presence of dl-glyceraldehyde, they catalyzed nitrite-dependent O₂ evolution (mean of 13 preparations, 17.5 μmole per mg chlorophyll per hour, sd 3.64). The optimum concentration of nitrite was 0.5 mm; 0.12 mm nitrite supported V_max/2. The reaction was accompanied by the consumption of nitrite; 55 to 80% of the nitrite-N consumed was recovered as ammonia. In short experiments (less than 10 minutes) the O₂ to nitrite ratio approached 1.5, but thereafter decreased. There was no nitrite-dependent O₂ evolution with chloroplasts from plants grown without added nitrate but such chloroplasts could assimilate ammonia at about the usual rate. The results are consistent with the reduction of nitrite to ammonia involving nitrate-induced nitrite reductase and a reductant generated by the chloroplast electron transport chain.     

A semantic analysis of the annotations of the human genome

The correct interpretation of any biological experiment depends in an essential way on the accuracy and consistency of the existing annotation databases. Such databases are ubiquitous and used by all life scientists in most experiments. However, it is well known that such databases are incomplete and many annotations may also be incorrect. In this paper we describe a technique that can be used to analyze the semantic content of such annotation databases. Our approach is able to extract implicit semantic relationships between genes and functions. This ability allows us to discover novel functions for known genes. This approach is able to identify missing and inaccurate annotations in existing annotation databases, and thus help improve their accuracy. We used our technique to analyze the current annotations of the human genome. From this body of annotations, we were able to predict 212 additional gene-function assignments. A subsequent literature search found that 138 of these gene-functions assignments are supported by existing peer-reviewed papers. An additional 23 assignments have been confirmed in the meantime by the addition of the respective annotations in later releases of the Gene Ontology database. Overall, the 161 confirmed assignments represent 75.95% of the proposed gene-function assignments. Only one of our predictions (0.4%) was contradicted by the existing literature. We could not find any relevant articles for 50 of our predictions (23.58%). The method is independent of the organism and can be used to analyze and improve the quality of the data of any public or private annotation database.     

Electrophoretic identification of poritid species (Anthozoa: Scleractinia)

Electrophoretic surveys of 13 enzyme-coding loci distinguished unambiguously five morphologically defined species of Porites and two species of Goniopora. Each species was identifiable solely by unique, qualitative banding patterns at 1–6 loci. Genetic distances give preliminary estimates that these Porites species diverged from common ancestors 8–22 Ma during the Miocene, and that the two Goniopora species diverged about 3.5 Ma in the Pliocene, assuming Porites evolved from Goniopora 55 million years ago (Ma). Correspondence to: R. L. Garthwaite     

Species richness and community structure of reef-building corals on the nearshore Great Barrier Reef

Species richness, cover and community structure of reef-building corals were assessed at 599 sites on 135 reefs along the Great Barrier Reef (GBR) between 1994 and 2001, with focus on the nearshore area. Communities were described hierarchically, with smaller regional communities forming part of higher level communities at increasing spatial scales. Site richness increased from the coast to the mid-continental shelf, declining on the outer shelf. Richness also increased with depth to 5 m, stabilizing thereafter. An anomaly was present in a 400 km section adjacent to the northern, ‘wet tropics’ coast, where site richness was 67 and 41% lower than the adjacent far northern and central GBR, respectively; this was probably due to the disturbance regime, with an apparent anthropogenic component. Site richness also declined in the Southern GBR, probably due to naturally marginal conditions. All indicator species had highest values in five small Far Northern and Central GBR communities. In the eight depauperate communities no indicator species had high values, indicating that these communities represent degraded, yet potentially transitional forms of the more diverse communities of the Far Northern and Central GBR. The study shows that on the GBR, disturbance results in the local removal of corals rather than a shift to suites of other coral species.     

Th1-Th17 Cells Contribute to the Development of Uropathogenic Escherichia coli-Induced Chronic Pelvic Pain

The etiology of chronic prostatitis/chronic pelvic pain syndrome in men is unknown but may involve microbes and autoimmune mechanisms. We developed an infection model of chronic pelvic pain in NOD/ShiLtJ (NOD) mice with a clinical Escherichia coli isolate (CP-1) from a patient with chronic pelvic pain. We investigated pain mechanisms in NOD mice and compared it to C57BL/6 (B6) mice, a strain resistant to CP-1-induced pain. Adoptive transfer of CD4+ T cells, but not serum, from CP-1-infected NOD mice was sufficient to induce chronic pelvic pain. CD4+ T cells in CP-1-infected NOD mice expressed IFN-γ and IL-17A but not IL-4, consistent with a Th1/Th17 immune signature. Adoptive transfer of ex-vivo expanded IFN-γ or IL-17A-expressing cells was sufficient to induce pelvic pain in naïve NOD recipients. Pelvic pain was not abolished in NOD-IFN-γ-KO mice but was associated with an enhanced IL-17A immune response to CP1 infection. These findings demonstrate a novel role for Th1 and Th17-mediated adaptive immune mechanisms in chronic pelvic pain.     

TRADD contributes to tumour suppression by regulating ULF-dependent p19Arf ubiquitylation

Tumour necrosis factor receptor (TNFR)-associated death domain (TRADD) protein is a central adaptor in the TNFR1 signalling complex that mediates both cell death and inflammatory signals. Here, we report that Tradd deficiency in mice accelerated tumour formation in a chemical-induced carcinogenesis model independently of TNFR1 signalling. In vitro, primary cells lacking TRADD were less susceptible to HRas-induced senescence and showed a reduced level of accumulation of the p19(Arf) tumour suppressor protein. Our data indicate that TRADD shuttles dynamically from the cytoplasm into the nucleus to modulate the interaction between p19(Arf) and its E3 ubiquitin ligase ULF, thereby promoting p19(Arf) protein stability and tumour suppression. These results reveal a previously unknown tumour-suppressive role for nuclear TRADD, augmenting its long-established cytoplasmic functions in inflammatory and immune signalling cascades. Our findings also make an important contribution to the rapidly expanding field of p19(Arf) post-translational regulation.     

O-antigen modulates infection-induced pain States

The molecular initiators of infection-associated pain are not understood. We recently found that uropathogenic E. coli (UPEC) elicited acute pelvic pain in murine urinary tract infection (UTI). UTI pain was due to E. coli lipopolysaccharide (LPS) and its receptor, TLR4, but pain was not correlated with inflammation. LPS is known to drive inflammation by interactions between the acylated lipid A component and TLR4, but the function of the O-antigen polysaccharide in host responses is unknown. Here, we examined the role of O-antigen in pain using cutaneous hypersensitivity (allodynia) to quantify pelvic pain behavior and using sacral spinal cord excitability to quantify central nervous system manifestations in murine UTI. A UPEC mutant defective for O-antigen biosynthesis induced chronic allodynia that persisted long after clearance of transient infections, but wild type UPEC evoked only acute pain. E. coli strains lacking O-antigen gene clusters had a chronic pain phenotype, and expressing cloned O-antigen gene clusters altered the pain phenotype in a predictable manner. Chronic allodynia was abrogated in TLR4-deficient mice, but inflammatory responses in wild type mice were similar among E. coli strains spanning a wide range of pain phenotypes, suggesting that O-antigen modulates pain independent of inflammation. Spinal cords of mice with chronic allodynia exhibited increased spontaneous firing and compromised short-term depression, consistent with centralized pain. Taken together, these findings suggest that O-antigen functions as a rheostat to modulate LPS-associated pain. These observations have implications for an infectious etiology of chronic pain and evolutionary modification of pathogens to alter host behaviors.     

Diversity of Scleractinia and Octocorallia in the mesophotic zone of the Great Barrier Reef, Australia

Mesophotic coral reefs in the Indo-West Pacific, the most diverse coral reef region on earth, are among the least documented. This study provides the first detailed investigation of the diversity of Scleractinia and Octocorallia of the mesophotic Great Barrier Reef (GBR). Specimens were collected by 100-m rock dredge tows at 47–163 m depth on 23 sites in four regions (15.3°–19.7° latitude South). Twenty-nine hard coral species from 19 families were recorded, with the greatest diversity found at <60 m depth, and no specimen was found >102 m. Many of these species are also commonly observed at shallower depths, particularly in inshore areas. Twenty-seven octocoral genera were collected, 25 of which represented azooxanthellate genera. Generic richness of octocorals was highest at depths >60 m. Sixteen of the 25 azooxanthellate genera were either absent or very rare at <18 m, and only five azooxanthellate genera were common on both shallow and mesophotic reefs. Species-area models indicated that the total diversity of hard corals on the deep mesophotic reefs sampled during this study was ~84 species while octocorals were represented by ~37 genera; however, the wide 95% confidence limits indicates that more intensive sampling effort is required to improve the accuracy of these estimates. Nonetheless, these results show that the taxonomic richness, particularly of hard corals, on mesophotic reefs may be much higher than previously thought, a finding that has implications for the comprehensive and adequate protection of the full range of biodiversity of the GBR.     

Predicting the Location and Spatial Extent of Submerged Coral Reef Habitat in the Great Barrier Reef World Heritage Area,Australia

Aim

Coral reef communities occurring in deeper waters have received little research effort compared to their shallow-water counterparts, and even such basic information as their location and extent are currently unknown throughout most of the world. Using the Great Barrier Reef as a case study, habitat suitability modelling is used to predict the distribution of deep-water coral reef communities on the Great Barrier Reef, Australia. We test the effectiveness of a range of geophysical and environmental variables for predicting the location of deep-water coral reef communities on the Great Barrier Reef.

Location

Great Barrier Reef, Australia.

Methods

Maximum entropy modelling is used to identify the spatial extent of two broad communities of habitat-forming megabenthos phototrophs and heterotrophs. Models were generated using combinations of geophysical substrate properties derived from multibeam bathymetry and environmental data derived from Bio-ORACLE, combined with georeferenced occurrence records of mesophotic coral communities from autonomous underwater vehicle, remotely operated vehicle and SCUBA surveys. Model results are used to estimate the total amount of mesophotic coral reef habitat on the GBR.

Results

Our models predict extensive but previously undocumented coral communities occurring both along the continental shelf-edge of the Great Barrier Reef and also on submerged reefs inside the lagoon. Habitat suitability for phototrophs is highest on submerged reefs along the outer-shelf and the deeper flanks of emergent reefs inside the GBR lagoon, while suitability for heterotrophs is highest in the deep waters along the shelf-edge. Models using only geophysical variables consistently outperformed models incorporating environmental data for both phototrophs and heterotrophs.

Main Conclusion

Extensive submerged coral reef communities that are currently undocumented are likely to occur throughout the Great Barrier Reef. High-quality bathymetry data can be used to identify these reefs, which may play an important role in resilience of the GBR ecosystem to climate change.