The unstructured C-terminus of the tau subunit of Escherichia coli DNA polymerase III holoenzyme is the site of interaction with the alpha subunit

The τ subunit of Escherichia coli DNA polymerase III holoenzyme interacts with the α subunit through its C-terminal Domain V, τ_C16. We show that the extreme C-terminal region of τ_C16 constitutes the site of interaction with α. The τ_C16 domain, but not a derivative of it with a C-terminal deletion of seven residues (τ_C16Δ7), forms an isolable complex with α. Surface plasmon resonance measurements were used to determine the dissociation constant (K_D) of the α−τ_C16 complex to be ~260pM. Competition with immobilized τ_C16 by τ_C16 derivatives for binding to α gave values of K_D of 7μM for the α−τ_C16Δ7 complex. Low-level expression of the genes encoding τ_C16 and τ_C167, but not τ_C16Δ11, is lethal to E. coli. Suppression of this lethal phenotype enabled selection of mutations in the 3′ end of the τ_C16 gene, that led to defects in α binding. The data suggest that the unstructured C-terminus of τ becomes folded into a helix–loop–helix in its complex with α. An N-terminally extended construct, τ_C24, was found to bind DNA in a salt-sensitive manner while no binding was observed for τ_C16, suggesting that the processivity switch of the replisome functionally involves Domain IV of τ.     

A new perspective on the function of Tissue Non-Specific Alkaline Phosphatase: from bone mineralization to intra-cellular lipid accumulation

Molecular and Cellular Biochemistry - Tissue-nonspecific alkaline phosphatase (TNAP) is one of four isozymes, which include germ cell, placental and intestinal alkaline phosphatases. The TNAP...     

Using multiple‐source occurrence data to identify patterns and drivers of decline in arid‐dwelling Australian marsupials

Many of the world's terrestrial mammal species are imperilled, but recent extinctions and declines have been most severe in Australia. In particular, arid‐dwelling marsupials in a critical weight range (35–5500 g) have declined dramatically following European settlement. In the absence of long‐term monitoring, documenting these declines or distribution shifts and their causes often relies on occurrence data from multiple sources. Using atlas records, we compared the distributions of all currently extant marsupials in the critical weight range in Australia's arid Northern Territory pre‐ and post‐1975. For taxa with evidence of range contraction, we evaluated alternative hypotheses to explain this contraction (i.e. competition, predation, productivity, climate) using several techniques to improve our confidence in the results. Despite a substantial increase in the number of mammal records across the study region post‐1975, the bilby Macrotis lagotis and desert form of the common brushtail possum Trichosurus vulpecula appear to have contracted in distribution by 25 and 40%, respectively. These changes in distribution were best explained by hypotheses of competition and climate‐change, respectively. Macrotis lagotis was more likely to occur on land without a history of cattle grazing and with low rabbit densities, while T. vulpecula has contracted to parts of its distribution that experience cooler maximum temperatures over the hottest months of the year. For five other taxa (including the vulnerable black‐footed rock‐wallaby Petrogale lateralis) we recorded increases in distribution post‐1975, probably reflecting increased survey effort rather than actual range expansion. We conclude that models using multiple‐source occurrence data can provide key insights into the patterns and drivers of contemporary species’ declines, and represent useful tools for conservation.     

Sex and age differences in habitat use by invasive cane toads (Rhinella marina) and a native anuran (Cyclorana australis) in the Australian wet–dry tropics

Although generalized habitat use may contribute to the success of invasive taxa, even species that are typically described as habitat generalists exhibit non‐random patterns of habitat use. We measured abiotic and biotic factors in 42 plots (each 100 × 10 m) along a 4.2‐km long unpaved road in tropical Australia, at a site that had been invaded by cane toads (Rhinella marina Bufonidae) seven years previously. We also counted anurans at night in each of these plots on 103 nights during the tropical wet season, over a five‐year period, beginning soon after the initial toad invasion. Spatial distributions differed significantly among adult male toads (n = 1047), adult female toads (n = 1222), juvenile toads (n = 342) and native frogs (Cyclorana australis Hylidae, n = 234). Adult male toads were closely associated with water bodies used as calling and/or spawning sites, whereas adult female toads and native frogs were most commonly encountered in drier forested areas on sloping ground. Juvenile toads used the margins of the floodplain more than conspecific adults did, but the floodplain itself was rarely used. Understanding which components of the habitat are most important to specific age and sex classes within a population, or how invasive species differ from native species in this respect, can clarify issues such as the spatial and temporal location of ecological impact by an invader, and the most effective places for control of the invader with minimal collateral effects on the native biota.     

Impact of increasing capacity for generating and using research on maternal and perinatal health practices in South East Asia (SEA-ORCHID Project)

Background

Maternal and neonatal mortality and morbidity remain unacceptably high in many low and middle income countries. SEA-ORCHID was a five year international collaborative project in South East Asia which aimed to determine whether health care and health outcomes for mothers and babies could be improved by developing capacity for research generation, synthesis and use.

Methods

Nine hospitals in Indonesia, Malaysia, the Philippines and Thailand participated in SEA-ORCHID. These hospitals were supported by researchers from three Australian centres. Health care practices and outcomes were assessed for 1000 women at each hospital both before and after the intervention. The capacity development intervention was tailored to the needs and context of each hospital and delivered over an 18 month period. Main outcomes included adherence to forms of care likely to be beneficial and avoidance of forms of care likely to be ineffective or harmful.

Results

We observed substantial variation in clinical practice change between sites. The capacity development intervention had a positive impact on some care practices across all countries, including increased family support during labour and decreased perineal shaving before birth, but in some areas there was no significant change in practice and a few beneficial practices were followed less often.

Conclusion

The results of SEA-ORCHID demonstrate that investing in developing capacity for research use, synthesis and generation can lead to improvements in maternal and neonatal health practice and highlight the difficulty of implementing evidence-based practice change.     

Determination of partial amino acid composition from tandem mass spectra for use in peptide identification strategies

We demonstrate a new approach to the determination of amino acid composition from tandem mass spectrometrically fragmented peptides using both experimental and simulated data. The approach has been developed to be used as a search-space filter in a protein identification pipeline with the aim of increased performance above that which could be attained by using immonium ion information. Three automated methods have been developed and tested: one based upon a simple peak traversal, in which all intense ion peaks are treated as being either a b- or y-ion using a wide mass tolerance; a second which uses a much narrower tolerance and does not perform transformations of ion peaks to the complementary type; and the unique fragments method which allows for b- or y-ion type to be inferred and corroborated using a scan of the other ions present in each peptide spectrum. The combination of these methods is shown to provide a high-accuracy set of amino acid predictions using both experimental and simulated data sets. These high quality predictions, with an accuracy of over 85%, may be used to identify peptide fragments that are hard to identify using other methods. The data simulation algorithm is also shown post priori to be a good model of noiseless tandem mass spectrometric peptide data.     

Protein and peptide identification algorithms using MS for use in high-throughput, automated pipelines

Current proteomics experiments can generate vast quantities of data very quickly, but this has not been matched by data analysis capabilities. Although there have been a number of recent reviews covering various aspects of peptide and protein identification methods using MS, comparisons of which methods are either the most appropriate for, or the most effective at, their proposed tasks are not readily available. As the need for high-throughput, automated peptide and protein identification systems increases, the creators of such pipelines need to be able to choose algorithms that are going to perform well both in terms of accuracy and computational efficiency. This article therefore provides a review of the currently available core algorithms for PMF, database searching using MS/MS, sequence tag searches and de novo sequencing. We also assess the relative performances of a number of these algorithms. As there is limited reporting of such information in the literature, we conclude that there is a need for the adoption of a system of standardised reporting on the performance of new peptide and protein identification algorithms, based upon freely available datasets. We go on to present our initial suggestions for the format and content of these datasets.     

Thrombin peptide (TP508) treatment of rat growth plate cartilage cells promotes proliferation and retention of the chondrocytic phenotype while blocking terminal endochondral differentiation

A synthetic peptide representing the receptor-binding domain of human thrombin (TP508, also known as Chrysalin) accelerates fracture repair in rats via endochondral ossification and promotes repair of rabbit cartilage defects. To understand how this peptide might stimulate cartilage and bone formation, we employed an established in vitro model of growth plate cartilage regulation. Rat costochondral cartilage resting zone and growth zone chondrocytes were treated with 0, 0.07, 0.7, or 7 microg/ml TP508 or a scrambled peptide, TP508-SP. Proliferation ([3H]-thymidine incorporation) was examined in pre-confluent cultures; effects on cell number, alkaline phosphatase activity, [35S]-sulfate incorporation, and responsiveness to vitamin D metabolites were tested using confluent cultures. TP508 did not affect proliferation of resting zone cells but it caused a dose-dependent increase in cell number and DNA synthesis of growth zone cells. Alkaline phosphatase specific activity of resting zone cells was reduced by TP508, whereas [35S]-sulfate incorporation was increased. Neither parameter was affected in growth zone cell cultures. TP508 treatment for 24 h did not induce resting zone cells to respond to 1alpha,25(OH)2D3, either with respect to alkaline phosphatase activity or proteoglycan production. In contrast, TP508 treatment reduced the stimulatory effect of 24R,25(OH)2D3 on alkaline phosphatase but it did not alter the stimulatory effect of 24R,25(OH)2D3 on [35S]-sulfate incorporation. In cultures treated for 48, 72, or 140 h with TP508, 1alpha,25(OH)2D3 restored alkaline phosphatase activity to control levels but did not stimulate activity over levels observed in untreated control cultures. The stimulatory effect of TP508 on [35S]-sulfate incorporation was evident up to 48 h post-confluence but at later time points, proteoglycan production was comparable to that seen in control cultures, control cultures challenged with 1alpha,25(OH)2D3, and cultures treated with TP508 followed by 1alpha,25(OH)2D3. TP508-SP had no effect on any of the parameters tested. These results indicate that TP508 exerts maturation specific effects on chondrocytes in the endochondral lineage, promoting cartilage extracellular matrix synthesis over endochondral differentiation in resting zone cells and proliferation over differentiation of growth zone cells.