Control of the exotic bulb, Yellow Soldier (Lachenalia reflexa) invading a Banksia woodland, Perth, Western Australia

Summary In recent times managers have become increasingly aware of the South African bulbous species Yellow Soldier ( Lachenalia reflexa ) becoming a serious weed of bushland on the Swan Coastal Plain. In 1998, trials were implemented to investigate control options for Yellow Soldier invading the understorey of a Banksia ( Banksia attenuata ) Woodland west of Perth. Our trials showed that hand removal over two seasons left all natives intact but was very labour intensive, only reducing cover of Yellow Soldier by 44%. It also triggered germination by ephemeral weeds. Wiping the leaves of individual plants with a 10% glyphosate solution was not effective and was also highly labour intensive. Spot spraying with metsulfuron methyl at 0.2 g/15 L (5 g/ha) reduced the cover of Yellow Soldier by 65%, was easier to implement and appeared to have had insignificant effects on natives. We hope that this trial will encourage other workers in the field to undertake controlled trials to refine treatments at restoration sites.     

Interactions between large African browsers and thorny Acacia on a wildlife ranch in Kenya

Some plants respond to browsing with compensatory regrowth of plant tissues and with increased thorn growth. Associations between browsers and their preferred forage were examined through wandering quarter vegetation sampling and observational studies in an effort to understand how some plants respond to browsing by large African herbivores. Acacia seyal (n = 2680) A. drepanolobium (n = 1850), and Balanites glabra (n = 960) were three species of frequently browsed indigenous plants examined on Game Ranching Ltd. in Kenya. There were several statistically significant associations revealed. Individual A. seyal exposed to intensive browser utilization were observed to lose shoot tips, produce long thorns, and have relatively few flowers and fruits. Browser utilization was associated with increased lateral branching in A. drepanolobium and with an increased occurrence of short, thickened spines in B. glabra. Thorns, spines and flowers were measurable indicators of relative browser utilization, and may be useful features to monitor in the management of large African mammals and their prickly forage     

Protein sequence similarity searches using patterns as seeds.

Protein families often are characterized by conserved sequence patterns or motifs. A researcher frequently wishes to evaluate the significance of a specific pattern within a protein, or to exploit knowledge of known motifs to aid the recognition of greatly diverged but homologous family members. To assist in these efforts, the pattern-hit initiated BLAST (PHI-BLAST) program described here takes as input both a protein sequence and a pattern of interest that it contains. PHI-BLAST searches a protein database for other instances of the input pattern, and uses those found as seeds for the construction of local alignments to the query sequence. The random distribution of PHI-BLAST alignment scores is studied analytically and empirically. In many instances, the program is able to detect statistically significant similarity between homologous proteins that are not recognizably related using traditional single-pass database search methods. PHI-BLAST is applied to the analysis of CED4-like cell death regulators, HS90-type ATPase domains, archaeal tRNA nucleotidyltransferases and archaeal homologs of DnaG-type DNA primases.     

Acid Orcein-Iron and Acid Orcein-Copper Stains for Elastin

Paraffin sections of formol-fixed tissues stained 4-18 hr in 70% alcohol containing 1% orcein and 1% of concentrated (12 N) HCl by volume yield the familiar purple brown elastin and red nuclei on a pink background. When sections so stained are transferred directly from the stain to 70% alcohol containing 0.02% ferric chloride (FeCl₃·6 H₂O) or 0.02% copper sulfate (CuSO₄·5 H₂O) for a 15 sec to 3 min period, elastin coloration is changed to black or reddish black and chromatin staining to reddish black. The procedure can be counterstained with picro-methyl blue to yield blue collagen and reticulum or with our flavianic acid, ferric chloride, acid fuchsin mixture to give deep yellow background and deep red collagen.     

The diversity of arthropods in homes across the United States as determined by environmental DNA analyses

We spend most of our lives inside homes, surrounded by arthropods that impact our property as pests and our health as disease vectors and producers of sensitizing allergens. Despite their relevance to human health and well‐being, we know relatively little about the arthropods that exist in our homes and the factors structuring their diversity. As previous work has been limited in scale by the costs and time associated with collecting arthropods and the subsequent morphological identification, we used a DNA‐based method for investigating the arthropod diversity in homes via high‐throughput marker gene sequencing of home dust. Settled dust samples were collected by citizen scientists from both inside and outside more than 700 homes across the United States, yielding the first continental‐scale estimates of arthropod diversity associated with our residences. We were able to document food webs and previously unknown geographic distributions of diverse arthropods – from allergen producers to invasive species and nuisance pests. Home characteristics, including the presence of basements, home occupants and surrounding land use, were more useful than climate parameters in predicting arthropod diversity in homes. These noninvasive, scalable tools and resultant findings not only provide the first continental‐scale maps of household arthropod diversity, but our analyses also provide valuable baseline information on arthropod allergen exposures and the distributions of invasive pests inside homes.     

Patterns of endemism of the eastern North American cave fauna

Aim Over 250 species of obligate terrestrial cave‐dwelling animals (troglobionts) are known from single caves in the eastern United States. We investigate their geographical distribution, especially in relation to other troglobionts. We relate these patterns to taxonomic group, opportunities for dispersal and geographical location. Location Caves of the United States east of the Mississippi River. Methods We associated over 3000 records of more than 450 troglobiotic species and subspecies with hexagons of 1000, 5000 and 10,000 km² in size. We calculated Moran's I, black–white joins and cubic regression of endemics on non‐endemics at all three spatial scales. For 5000 km² hexagons, we modelled the spatial autocorrelation of the residuals of the cubic regression of endemics on non‐endemics. Results Differences among orders in percentage single‐cave endemism were not significant, except for Pseudoscorpionida, which was higher (69%) than any other order. At all three scales, Moran's I and black–white joins were significant, indicating a clumped distribution of both single‐cave endemics and other troglobionts. Spatial patterns were similar at all three scales and Moran's I was highest at 5000 km². The cubic fit of endemics to non‐endemics was consistently better, with less systematic error or residuals, than were linear or quadratic models. Residuals showed a significant geographical pattern with excess endemics in more southerly locations. Main conclusions There was both a non‐spatial and spatial component to the pattern of single‐cave endemism. The non‐spatial component was the association of high levels of single‐cave endemism with areas of high diversity of non‐endemics. It may be that both are high because of high secondary productivity. Spatially, single‐cave endemism is high in central rather than peripheral areas and in the southern part of the range. It is not higher in areas of more dissected limestone, which would reduce migration rates; if anything endemism is lower. Regional spatial effects are important, indicating that cave communities cannot be understood (or protected) in isolation.     

Genetic Variation in Healthy Oldest-Old

Individuals who live to 85 and beyond without developing major age-related diseases may achieve this, in part, by lacking disease susceptibility factors, or by possessing resistance factors that enhance their ability to avoid disease and prolong lifespan. Healthy aging is a complex phenotype likely to be affected by both genetic and environmental factors. We sequenced 24 candidate healthy aging genes in DNA samples from 47 healthy individuals aged eighty-five years or older (the ‘oldest-old’), to characterize genetic variation that is present in this exceptional group. These healthy seniors were never diagnosed with cancer, cardiovascular disease, pulmonary disease, diabetes, or Alzheimer disease. We re-sequenced all exons, intron-exon boundaries and selected conserved non-coding sequences of candidate genes involved in aging-related processes, including dietary restriction (PPARG, PPARGC1A, SIRT1, SIRT3, UCP2, UCP3), metabolism (IGF1R, APOB, SCD), autophagy (BECN1, FRAP1), stem cell activation (NOTCH1, DLL1), tumor suppression (TP53, CDKN2A, ING1), DNA methylation (TRDMT1, DNMT3A, DNMT3B) Progeria syndromes (LMNA, ZMPSTE24, KL) and stress response (CRYAB, HSPB2). We detected 935 variants, including 848 single nucleotide polymorphisms (SNPs) and 87 insertion or deletions; 41% (385) were not recorded in dbSNP. This study is the first to present a comprehensive analysis of genetic variation in aging-related candidate genes in healthy oldest-old. These variants and especially our novel polymorphisms are valuable resources to test for genetic association in models of disease susceptibility or resistance. In addition, we propose an innovative tagSNP selection strategy that combines variants identified through gene re-sequencing- and HapMap-derived SNPs.     

Detecting microRNA activity from gene expression data

Background  

MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression by binding to the messenger RNA (mRNA) of protein coding genes. They control gene expression by either inhibiting translation or inducing mRNA degradation. A number of computational techniques have been developed to identify the targets of miRNAs. In this study we used predicted miRNA-gene interactions to analyse mRNA gene expression microarray data to predict miRNAs associated with particular diseases or conditions.