Preferential binding of human XPA to the mitomycin C-DNA interstrand crosslink and modulation by arsenic and cadmium

The Xeroderma Pigmentosum A (XPA) protein is involved in the DNA damage recognition and repair complex formation steps of nucleotide excision repair (NER), and has been shown to preferentially bind to various forms of DNA damage including bulky lesions. DNA interstrand crosslinks are of particular interest as a form of DNA damage, since these lesions involve both strands of duplex DNA and present special challenges to the repair machinery, and mitomycin C (MMC) is one of several useful cancer chemotherapy drugs that induce these lesions. Purified XPA and the minimal DNA-binding domain of XPA are both fully capable of preferentially binding to MMC-DNA interstrand crosslinks in the absence of other proteins from the NER complex. Circular dichroism (CD) and gel shift assays were used to investigate XPA-DNA binding and to assess changes in secondary structure induced as a consequence of the interaction of XPA with model MMC-crosslinked and unmodified DNAs. These studies revealed that while XPA demonstrates only a modest increase in affinity for adducted DNA, it adopts a different conformation when bound to MMC-damaged DNA than when bound to undamaged DNA. This change in conformation may be more important in recruiting other proteins into a competent NER complex at damaged sites than preferential binding per se. Arsenic had little effect on XPA binding even at toxic concentrations, whereas cadmium reduced XPA binding to DNA to 10-15% that of Zn-XPA, and zinc addition could only partially restore activity. In addition, there was little or no change in conformation when Cd-XPA bound MMC-crosslinked DNA even though it demonstrated preferential binding, which may contribute to the mechanism by which cadmium can act as a co-mutagen and co-carcinogen.     

The Argos-CLS Kalman Filter: Error Structures and State-Space Modelling Relative to Fastloc GPS Data

Understanding how an animal utilises its surroundings requires its movements through space to be described accurately. Satellite telemetry is the only means of acquiring movement data for many species however data are prone to varying amounts of spatial error; the recent application of state-space models (SSMs) to the location estimation problem have provided a means to incorporate spatial errors when characterising animal movements. The predominant platform for collecting satellite telemetry data on free-ranging animals, Service Argos, recently provided an alternative Doppler location estimation algorithm that is purported to be more accurate and generate a greater number of locations that its predecessor. We provide a comprehensive assessment of this new estimation process performance on data from free-ranging animals relative to concurrently collected Fastloc GPS data. Additionally, we test the efficacy of three readily-available SSM in predicting the movement of two focal animals. Raw Argos location estimates generated by the new algorithm were greatly improved compared to the old system. Approximately twice as many Argos locations were derived compared to GPS on the devices used. Root Mean Square Errors (RMSE) for each optimal SSM were less than 4.25km with some producing RMSE of less than 2.50km. Differences in the biological plausibility of the tracks between the two focal animals used to investigate the utility of SSM highlights the importance of considering animal behaviour in movement studies. The ability to reprocess Argos data collected since 2008 with the new algorithm should permit questions of animal movement to be revisited at a finer resolution.     

A European pest to control a new zealand weed: investigating the safety of heather beetle, Lochmaea suturalis (Coleoptera: Chrysomelidae) for biological control of heather, Calluna vulgaris

Heather, Calluna vulgaris (L.) Hull, is a serious invasive weed in the central North Island of New Zealand, especially in Tongariro National Park, a World Heritage Area. Heather beetle, Lochmaea suturalis (Thomson), is a foliage-feeding pest of Calluna in Europe, that was selected as the most promising biological control agent for introduction into New Zealand, because it causes high levels of damage to Calluna in Europe. Host-range tests indicated that L. suturalis poses a negligible threat to native New Zealand plants. Cultivars of Calluna grown as ornamentals are suitable food plants, but are unlikely to be severely affected because L. suturalis requires a damp understorey of moss or litter for successful oviposition and pupation, which is rarely present in gardens. However, mosses and litter occurring under Calluna stands in Tongariro National Park are suitable substrates for eggs and pupae. Lochmaea suturalis released in New Zealand has been freed of parasitoids and a microsporidian disease that attack the beetles in Europe.     

Shotgun metagenomics and microscopy indicate diverse cyanophytes,other bacteria,and microeukaryotes in the epimicrobiota of a northern Chilean wetland Nostoc (Cyanobacteria)

Prokaryotic Nostoc, one of the world's most conspicuous and widespread algal genera (similar to eukaryotic algae, plants, and animals) is known to support a microbiome that influences host ecological roles. Past taxonomic characterizations of surface microbiota (epimicrobiota) of free‐living Nostoc sampled from freshwater systems employed 16S rRNA genes, typically amplicons. We compared taxa identified from 16S, 18S, 23S, and 28S rRNA gene sequences filtered from shotgun metagenomic sequence and used microscopy to illuminate epimicrobiota diversity for Nostoc sampled from a wetland in the northern Chilean Altiplano. Phylogenetic analysis and rRNA gene sequence abundance estimates indicated that the host was related to Nostoc punctiforme PCC 73102. Epimicrobiota were inferred to include 18 epicyanobacterial genera or uncultured taxa, six epieukaryotic algal genera, and 66 anoxygenic bacterial genera, all having average genomic coverage ≥90X. The epicyanobacteria Geitlerinemia, Oscillatoria, Phormidium, and an uncultured taxon were detected only by 16S rRNA gene; Gloeobacter and Pseudanabaena were detected using 16S and 23S; and Phormididesmis, Neosynechococcus, Symphothece, Aphanizomenon, Nodularia, Spirulina, Nodosilinea, Synechococcus, Cyanobium, and Anabaena (the latter corroborated by microscopy), plus two uncultured cyanobacterial taxa (JSC12, O77) were detected only by 23S rRNA gene sequences. Three chlamydomonad and two heterotrophic stramenopiles genera were inferred from 18S; the streptophyte green alga Chaetosphaeridium globosum was detected by microscopy and 28S rRNA genes, but not 18S rRNA genes. Overall, >60% of epimicrobial taxa were detected by markers other than 16S rRNA genes. Some algal taxa observed microscopically were not detected from sequence data. Results indicate that multiple taxonomic markers derived from metagenomic sequence data and microscopy increase epimicrobiota detection.     

Unknown New Zealand angiosperm assigned toCunoniaceae using sequence of the chloroplastrbcL gene

We report the first example of identification of an unknown flowering plant to family level using comparison of DNA sequences. The newly-discovered New Zealand plant had not been identified by traditional methods, but has been placed in the Gondwanic familyCunoniaceae on the basis of the sequence of its chloroplastrbcL gene. It has not flowered, but its vegetative characters are typical of the family. However, it is clearly unusual in several morphological and anatomical features and appears to match no known genus. We consider that, although it probably represents an unnamed new genus, it could possibly be a mutant dwarf form ofWeinmannia racemosa, so it is not prudent to name it at this time.     

Sickness certification system in the United Kingdom: qualitative study of views of general practitioners in Scotland

Objectives To explore how general practitioners operate the sickness certification system, their views on the system, and suggestions for change.Design Qualitative focus group study consisting of 11 focus groups with 67 participants.Setting General practitioners in practices in Glasgow, Tayside, and Highland regions, Scotland.Sample Purposive sample of general practitioners, with further theoretical sampling of key informant general practitioners to examine emerging themes.Results General practitioners believed that the sickness certification system failed to address complex, chronic, or doubtful cases. They seemed to develop various operational strategies for its implementation. There appeared to be important deliberate misuse of the system by general practitioners, possibly related to conflicts about roles and incongruities in the system. The doctor-patient relationship was perceived to conflict with the current role of general practitioners in sickness certification. When making decisions about certification, the general practitioners considered a wide variety of factors. They experienced contradictory demands from other system stakeholders and felt blamed for failing to make impossible reconciliations. They clearly identified the difficulties of operating the system when there was no continuity of patient care. Many wished either to relinquish their gatekeeper role or to continue only with major changes.Conclusions Policy makers need to recognise and accommodate the range and complexity of factors that influence the behaviour of general practitioners operating as gatekeepers to the sickness certification system, before making changes. Such changes are otherwise unlikely to result in improvement. Models other than the primary care gatekeeper model should be considered.     

Stormwater drainage pipes as a threat to a stream-dwelling amphipod of conservation significance, Austrogammarus australis, in southeastern Australia

The general hypothesis that catchment urbanization explained the distribution of the threatened, stream-dwelling amphipod Austrogammarus australis (listed under the Victorian Flora and Fauna Guarantee Act 1988) was tested using several surveys of 58 sites in streams draining the Dandenong Ranges on the eastern fringe of Melbourne, Victoria, Australia. More specifically, four catchment-scale elements of urban land, hypothesized as sources of stress to receiving streams, were separated: catchment imperviousness, drainage connection (proportion of impervious areas connected to streams by stormwater pipes), density of unsealed roads and density of septic tanks. The degree to which each attribute independently and jointly explained the occurrence of A. australis was assessed using hierarchical partitioning of logistic regression analyses. Drainage connection independently best explained the occurrence of A. australis, pointing to stormwater drainage design as the priority area of catchment management for the conservation of the species. The separation of urban land use into attributes that characterize likely stressor sources provides a useful framework for assessing and prioritizing the most appropriate management actions to minimize urban-related stresses to aquatic biota.     

A Validated Genome Wide Association Study to Breed Cattle Adapted to an Environment Altered by Climate Change

Continued production of food in areas predicted to be most affected by climate change, such as dairy farming regions of Australia, will be a major challenge in coming decades. Along with rising temperatures and water shortages, scarcity of inputs such as high energy feeds is predicted. With the motivation of selecting cattle adapted to these changing environments, we conducted a genome wide association study to detect DNA markers (single nucleotide polymorphisms) associated with the sensitivity of milk production to environmental conditions. To do this we combined historical milk production and weather records with dense marker genotypes on dairy sires with many daughters milking across a wide range of production environments in Australia. Markers associated with sensitivity of milk production to feeding level and sensitivity of milk production to temperature humidity index on chromosome nine and twenty nine respectively were validated in two independent populations, one a different breed of cattle. As the extent of linkage disequilibrium across cattle breeds is limited, the underlying causative mutations have been mapped to a small genomic interval containing two promising candidate genes. The validated marker panels we have reported here will aid selection for high milk production under anticipated climate change scenarios, for example selection of sires whose daughters will be most productive at low levels of feeding.