Diversity and Abundance of Club and Coral Fungi in the Upper Lane Cove Valley

The Kingdom Fungi are central players in the ecology and biogeochemistry of terrestrial ecosystems. Despite this importance, the diversity, distribution and abundance of fungal species are poorly known. Here, we undertook an intensive survey of club and coral fungi in the Upper Lane Cove Valley, Sydney, Australia. Over a two-year period, we collected more than 1100 specimens, and identified these to genus using a combination of DNA barcoding and morphology. The majority of specimens did not match any sequences in GenBank at more than 95% similarity, meaning that many of these fungi are either poorly represented in DNA databases, or are potentially novel species. A number of hotspots for fungal diversity and abundance were identified, largely along creek lines draining southwest through coachwood dominated vegetation. Notably, these hotspots all lie outside the adjacent Lane Cove National Park

A new framework of spatial targeting for single-species conservation planning

Context: Organisations acting to conserve and protect species across large spatial scales prioritise to optimise use of resources. Spatial conservation prioritization tools typically focus on identifying areas containing species groups of interest, with few tools used to identify the best areas for single-species conservation, in particular, to conserve currently widespread but declining species. / Objective: A single-species prioritization framework, based on temporal and spatial patterns of occupancy and abundance, was developed to spatially prioritize conservation action for widespread species by identifying smaller areas to work within to achieve predefined conservation objectives. / Methods: We demonstrate our approach for 29 widespread bird species in the UK, using breeding bird atlas data from two periods to define distribution, relative abundance and change in relative abundance. We selected occupied 10-km squares with abundance trends that matched species conservation objectives relating to maintaining or increasing population size or range, and then identified spatial clusters of squares for each objective using a Getis-Ord-Gi* or near neighbour analysis. / Results: For each species, the framework identified clusters of 20-km squares that enabled us to identify small areas in which species recovery action could be prioritized. / Conclusions: Our approach identified a proportion of species’ ranges to prioritize for species recovery. This approach is a relatively quick process that can be used to inform single-species conservation for any taxa if sufficiently fine-scale occupancy and abundance information is available for two or more time periods. This is a relatively simple first step for planning single-species focussed conservation to help optimise resource use

The risk of extinction for birds in Great Britain

t Over the last 20 years,species priorities for bird conservation in the UK have been guided by ‘Birds of Conservation Concern’ – an in-depth assessment made possible by the top-class data available on the status of the UK’s birds. For other wildlife, priorities tend to be informed by measures of extinction risk, generated by the IUCN Regional Red List process.We carried out the first formal IUCN assessment for birds in Great Britain. Of the 241 species assessed, 100 (43%) had at least one population (breeding and/or non-breeding) that qualified as Threatened using the standard IUCN Red List criteria and categories. Of 289 separate assessments of breeding or non-breeding populations, 39% qualified as Threatened (8% Critically Endangered, 14% Endangered, 17% Vulnerable) with a further 10% classified as Near Threatened. Both Golden Oriole Oriolus oriolus and Fieldfare Turdus pilaris were assessed as being Critically Endangered (Possibly Extinct) as breeding species, in addition to seven species that are already extinct (either Extinct or Regionally Extinct). The proportion of GB birds qualifying as Threatened was high compared with birds elsewhere in Europe and other taxonomic groups in GB. We believe that, if similar data were available, levels of extinction risk would be higher for other areas/taxa than is currently estimated

Genetic differentiation in the threatened soft coral Dendronephthya australis in temperate eastern Australia

The endangered soft coral Dendronephthya australis faces substantial population decreases in central eastern Australian waters. Despite uncertainty about the cause of these declines, the population genetics of the species has not been investigated. Genetic analysis suggests that D. australis is a single species within the family Nephtheidae, confirming identifications based on morphological characteristics only. Soft coral colonies were distributed from Seahorse Gardens in Port Stephens to Jervis Bay in temperate Australian waters, a distance of some 400 km. Genetic differentiation was observed along this distribution using SNP genotyping. Relatively high levels of genetic differentiation were observed between Jervis Bay and the other sites, indicating limited gene flow between this location and others. Moreover, the genetic distinctiveness, low diversity and heterozygote excess at this southern location suggested that it was subjected to a recent population decline and genetic bottleneck. Colonies at Seahorse Gardens and Ettalong, approximately 150 km south of Seahorse Gardens, displayed greater genetic diversity, making these sites more likely to host ancestral populations and to have acted as refugia. Recent substantial decreases in population sizes at these locations are particularly concerning, and these locations require immediate conservation attention

The Impact of Spatial Orientation Changes on Driving Behavior in Healthy Aging

Objectives Global cognitive changes in older age affect driving behavior and road safety, but how spatial orientation differences affect driving behaviors is unknown on a population level, despite clear implications for driving policy and evaluation during aging. The present study aimed to establish how spatial navigation changes affect driving behavior and road safety within a large cohort of older adults. Methods Eight hundred and four participants (mean age: 71.05) were recruited for a prospective cohort study. Participants self-reported driving behavior followed by spatial orientation (allocentric and egocentric) testing and a broader online cognitive battery (visuomotor speed, processing speed, executive functioning, spatial working memory, episodic memory, visuospatial functioning). Results Spatial orientation performance significantly predicted driving difficulty and frequency. Experiencing more driving difficulty was associated with worse allocentric spatial orientation, processing speed, and source memory performance. Similarly, avoiding challenging driving situations was associated with worse spatial orientation and episodic memory. Allocentric spatial orientation was the only cognitive domain consistently affecting driving behavior in under 70 and over 70 age groups, a common age threshold for driving evaluation in older age. Discussion We established for the first time that worse spatial orientation performance predicted increased driving difficulty and avoidance of challenging situations within an older adult cohort. Deficits in spatial orientation emerge as a robust indicator of driving performance in older age, which should be considered in future aging driving assessments, as it has clear relevance for road safety within the aging population

Are Ethnic and Gender Specific Equations Needed to Derive Fat Free Mass from Bioelectrical Impedance in Children of South Asian, Black African-Caribbean and White European Origin? Results of the Assessment of Body Composition in Children Study

Background Bioelectrical impedance analysis (BIA) is a potentially valuable method for assessing lean mass and body fat levels in children from different ethnic groups. We examined the need for ethnic- and gender-specific equations for estimating fat free mass (FFM) from BIA in children from different ethnic groups and examined their effects on the assessment of ethnic differences in body fat. Methods Cross-sectional study of children aged 8–10 years in London Primary schools including 325 South Asians, 250 black African-Caribbeans and 289 white Europeans with measurements of height, weight and arm-leg impedance (Z; Bodystat 1500). Total body water was estimated from deuterium dilution and converted to FFM. Multilevel models were used to derive three types of equation {A: FFM = linear combination(height+weight+Z); B: FFM = linear combination(height2/Z); C: FFM = linear combination(height2/Z+weight)}. Results Ethnicity and gender were important predictors of FFM and improved model fit in all equations. The models of best fit were ethnicity and gender specific versions of equation A, followed by equation C; these provided accurate assessments of ethnic differences in FFM and FM. In contrast, the use of generic equations led to underestimation of both the negative South Asian-white European FFM difference and the positive black African-Caribbean-white European FFM difference (by 0.53 kg and by 0.73 kg respectively for equation A). The use of generic equations underestimated the positive South Asian-white European difference in fat mass (FM) and overestimated the positive black African-Caribbean-white European difference in FM (by 4.7% and 10.1% respectively for equation A). Consistent results were observed when the equations were applied to a large external data set. Conclusions Ethnic- and gender-specific equations for predicting FFM from BIA provide better estimates of ethnic differences in FFM and FM in children, while generic equations can misrepresent these ethnic differences

Methods for microbial DNA extraction from soil for PCR amplification

Amplification of DNA from soil is often inhibited by co-purified contaminants. A rapid, inexpensive, large-scale DNA extraction method involving minimal purification has been developed that is applicable to various soil types (1). DNA is also suitable for PCR amplification using various DNA targets. DNA was extracted from 100g of soil using direct lysis with glass beads and SDS followed by potassium acetate precipitation, polyethylene glycol precipitation, phenol extraction and isopropanol precipitation. This method was compared to other DNA extraction methods with regard to DNA purity and size

A synthesis of bacterial and archaeal phenotypic trait data.

A synthesis of phenotypic and quantitative genomic traits is provided for bacteria and archaea, in the form of a scripted, reproducible workflow that standardizes and merges 26 sources. The resulting unified dataset covers 14 phenotypic traits, 5 quantitative genomic traits, and 4 environmental characteristics for approximately 170,000 strain-level and 15,000 species-aggregated records. It spans all habitats including soils, marine and fresh waters and sediments, host-associated and thermal. Trait data can find use in clarifying major dimensions of ecological strategy variation across species. They can also be used in conjunction with species and abundance sampling to characterize trait mixtures in communities and responses of traits along environmental gradients

Paclitaxel resistance is associated with switch from apoptotic to autophagic cell death in MCF-7 breast cancer cells

Taxanes remain first line chemotherapy in management of metastatic breast cancer and have a key role in epithelial ovarian cancer, with increasingly common use of weekly paclitaxel dosing regimens. However, their clinical utility is limited by the development of chemoresistance. To address this, we modelled in vitro paclitaxel resistance in MCF-7 cells. We show that at clinically relevant drug doses, emerging paclitaxel resistance is associated with profound changes in cell death responses and a switch from apoptosis to autophagy as the principal mechanism of drug-induced cytotoxicity. This was characterised by a complete absence of caspase-mediated apoptotic cell death (using the pan-caspase-inhibitor Z-VAD) in paclitaxel-resistant MCF-7TaxR cells, compared with parent MCF-7 or MDA-MB-231 cell lines on paclitaxel challenge, downregulation of caspase-7, caspase-9 and BCl2-interacting mediator of cell death (BIM) expression. Silencing with small interfering RNA to BIM in MCF-7 parental cells was sufficient to confer paclitaxel resistance, inferring the significance in downregulation of this protein in contributing to the resistant phenotype of the MCF-7TaxR cell line. Conversely, there was an increased autophagic response in the MCF-7TaxR cell line with reduced phospho-mTOR and relative resistance to the mTOR inhibitors rapamycin and RAD001. In conclusion, we show for the first time that paclitaxel resistance is associated with profound changes in cell death response with deletion of multiple apoptotic factors balanced by upregulation of the autophagic pathway and collateral sensitivity to platinum

The influence of the accessory genome on bacterial pathogen evolution

Bacterial pathogens exhibit significant variation in their genomic content of virulence factors. This reflects the abundance of strategies pathogens evolved to infect host organisms by suppressing host immunity. Molecular arms-races have been a strong driving force for the evolution of pathogenicity, with pathogens often encoding overlapping or redundant functions, such as type III protein secretion effectors and hosts encoding ever more sophisticated immune systems. The pathogens’ frequent exposure to other microbes, either in their host or in the environment, provides opportunities for the acquisition or interchange of mobile genetic elements. These DNA elements accessorise the core genome and can play major roles in shaping genome structure and altering the complement of virulence factors. Here, we review the different mobile genetic elements focusing on the more recent discoveries and highlighting their role in shaping bacterial pathogen evolution