Accurate whole human genome sequencing using reversible terminator chemistry

DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30x average depth of paired 35-base reads. We characterize four million single-nucleotide polymorphisms and four hundred thousand structural variants, many of which were previously unknown. Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.     

Effectiveness of phosphocitrate and N-sulpho-2-amino tricarballylate,a new analogue of phosphocitrate,in blocking hydroxyapatite induced crystal growth and calcium accumulation by matrix vesicles

Summary Phosphocitrate and its analogue N-sulpho-2-amino tricarballylate were compared with ethane-1-hydroxy-1, 1-diphosphonate for inhibition of calcium phosphate crystallization in hydroxyapatite induced crystal growth and⁴⁵Ca uptake by matrix vesicles. Phosphocitrate (1 M) was the most potent inhibitor followed by ethane-1-hydroxy-1, 1-diphosphonate and N-sulpho-2-amino tricarballylate, the latter requiring a high concentration (100 M) to be equally effective as an inhibitor.Acknowledgments. We wish to thank Mr J. Jordan and Miss L.C. Ward for the excellent technical assistance and Mr R.J. Tennant for the transmission electron microscopy. We also thank the Golden Poultry Farming Industries Ltd., Hobart, Tasmania for their generous supply of broiler strain chickens.     

The Molecule Pages database

The Alliance for Cellular Signaling (AfCS)-Nature Molecule Pages will be a comprehensive database of key facts about more than 3,000 proteins involved in cell signalling. Each entry will be created by invited experts and be peer-reviewed. Alongside the large-scale experiments being conducted by the AfCS scientists, the wealth of information contained in this database offers the potential of accelerating the pace of discovery in signal transduction research.     

An equilibrium-dependent retroviral mRNA switch regulates translational recoding

Most retroviruses require translational recoding of a viral messenger RNA stop codon to maintain a precise ratio of structural (Gag) and enzymatic (Pol) proteins during virus assembly. Pol is expressed exclusively as a Gag-Pol fusion either by ribosomal frameshifting or by read-through of the gag stop codon. Both of these mechanisms occur infrequently and only affect 5-10% of translating ribosomes, allowing the virus to maintain the critical Gag to Gag-Pol ratio. Although it is understood that the frequency of the recoding event is regulated by cis RNA motifs, no mechanistic explanation is currently available for how the critical protein ratio is maintained. Here we present the NMR structure of the murine leukaemia virus recoding signal and show that a protonation-dependent switch occurs to induce the active conformation. The equilibrium is such that at physiological pH the active, read-through permissive conformation is populated at approximately 6%: a level that correlates with in vivo protein quantities. The RNA functions by a highly sensitive, chemo-mechanical coupling tuned to ensure an optimal read-through frequency. Similar observations for a frameshifting signal indicate that this novel equilibrium-based mechanism may have a general role in translational recoding.     

Phosphorus partitioning and recovery of low-phosphorus iron-rich compounds through physical separation of Linz-Donawitz slag

The Linz-Donawitz (LD) steelmaking process produces LD slag at a rate of about 125 kg/t. After metallic scrap recovery, the non-metallic LD slag is rejected because its physical/chemical properties are unsuitable for recycling. X-ray diffraction (XRD) studies have indicated that non-metallic LD slag contains a substantial quantity of mineral phases such as di- and tricalcium silicates. The availability of these mineral phases indicates that LD slag can be recycled by iron (Fe)-ore sintering. However, the presence of 1.2wt% phosphorus (P) in the slag renders the material unsuitable for sintering operations. Electron probe microscopic analysis (EPMA) studies indicated concentration of phosphorus in dicalcium silicate phase as calcium phosphate. The Fe-bearing phases (i.e., wustite and dicalcium ferrite) showed comparatively lower concentrations of P compared with other phases in the slag. Attempts were made to lower the P content of LD slag by adopting various beneficiation techniques. Dry high-intensity magnetic separation and jigging were performed on as-received samples with particle sizes of 6 and 3 mm. Spiral separation was conducted using samples ground to sizes of less than 1 and 0.5 mm. Among these studies, grinding to 0.5 mm followed by spiral concentration demonstrated the best results, yielding a concentrate with about 0.75wt% P and 45wt% Fe.     

MicroRNAs can generate thresholds in target gene expression

MicroRNAs (miRNAs) are short, highly conserved noncoding RNA molecules that repress gene expression in a sequence-dependent manner. We performed single-cell measurements using quantitative fluorescence microscopy and flow cytometry to monitor a target gene's protein expression in the presence and absence of regulation by miRNA. We find that although the average level of repression is modest, in agreement with previous population-based measurements, the repression among individual cells varies dramatically. In particular, we show that regulation by miRNAs establishes a threshold level of target mRNA below which protein production is highly repressed. Near this threshold, protein expression responds sensitively to target mRNA input, consistent with a mathematical model of molecular titration. These results show that miRNAs can act both as a switch and as a fine-tuner of gene expression.     

Modulation of virulence within a pathogenicity island in vancomycin-resistant Enterococcus faecalis

Enterococci are members of the healthy human intestinal flora, but are also leading causes of highly antibiotic-resistant, hospital-acquired infection. We examined the genomes of a strain of Enterococcus faecalis that caused an infectious outbreak in a hospital ward in the mid-1980s (ref. 2), and a strain that was identified as the first vancomycin-resistant isolate in the United States, and found that virulence determinants were clustered on a large pathogenicity island, a genetic element previously unknown in this genus. The pathogenicity island, which varies only subtly between strains, is approximately 150 kilobases in size, has a lower G + C content than the rest of the genome, and is flanked by terminal repeats. Here we show that subtle variations within the structure of the pathogenicity island enable strains harbouring the element to modulate virulence, and that these variations occur at high frequency. Moreover, the enterococcal pathogenicity island, in addition to coding for most known auxiliary traits that enhance virulence of the organism, includes a number of additional, previously unstudied genes that are rare in non-infection-derived isolates, identifying a class of new targets associated with disease which are not essential for the commensal behaviour of the organism.     

Tartrate-resistant acid phosphatase deficiency causes a bone dysplasia with autoimmunity and a type I interferon expression signature

We studied ten individuals from eight families showing features consistent with the immuno-osseous dysplasia spondyloenchondrodysplasia. Of particular note was the diverse spectrum of autoimmune phenotypes observed in these individuals (cases), including systemic lupus erythematosus, Sj?gren's syndrome, hemolytic anemia, thrombocytopenia, hypothyroidism, inflammatory myositis, Raynaud's disease and vitiligo. Haplotype data indicated the disease gene to be on chromosome 19p13, and linkage analysis yielded a combined multipoint log(10) odds (LOD) score of 3.6. Sequencing of ACP5, encoding tartrate-resistant acid phosphatase, identified biallelic mutations in each of the cases studied, and in vivo testing confirmed a loss of expressed protein. All eight cases assayed showed elevated serum interferon alpha activity, and gene expression profiling in whole blood defined a type I interferon signature. Our findings reveal a previously unrecognized link between tartrate-resistant acid phosphatase activity and interferon metabolism and highlight the importance of type I interferon in the genesis of autoimmunity.     

Transvascular delivery of small interfering RNA to the central nervous system

A major impediment in the treatment of neurological diseases is the presence of the blood-brain barrier, which precludes the entry of therapeutic molecules from blood to brain. Here we show that a short peptide derived from rabies virus glycoprotein (RVG) enables the transvascular delivery of small interfering RNA (siRNA) to the brain. This 29-amino-acid peptide specifically binds to the acetylcholine receptor expressed by neuronal cells. To enable siRNA binding, a chimaeric peptide was synthesized by adding nonamer arginine residues at the carboxy terminus of RVG. This RVG-9R peptide was able to bind and transduce siRNA to neuronal cells in vitro, resulting in efficient gene silencing. After intravenous injection into mice, RVG-9R delivered siRNA to the neuronal cells, resulting in specific gene silencing within the brain. Furthermore, intravenous treatment with RVG-9R-bound antiviral siRNA afforded robust protection against fatal viral encephalitis in mice. Repeated administration of RVG-9R-bound siRNA did not induce inflammatory cytokines or anti-peptide antibodies. Thus, RVG-9R provides a safe and noninvasive approach for the delivery of siRNA and potentially other therapeutic molecules across the blood-brain barrier.     

Application of Scenario-based Approaches in Leadership Research: An Action Research Intervention as Three Sets of Interlinked Practices

This article illustrates how scenario planning (SP) and scenario analysis as can be conceptualised as practices contributing to an action research (AR) investigation of leadership development. The project described in this article was intended to strengthen leadership capacity in Australia’s rapidly changing aged care and community care sector. A research team comprising academics from three universities and managers from two faith-based not-for-profit organisations providing aged and community care participated in this study. As part of the research, two sets of scenario-based workshops were held: the first, to identify possible futures using SP; and the second, to deal with plausible scenarios these organisations are likely to face with the changes happening in the aged care environment in Australia by using scenario analysis. Although the researchers did not consider a link between practice theory and AR during the SP phase, practice theory became useful during the scenario analysis phase. The article includes a brief literature review followed by a discussion on the relationship between AR and practice theory. The processes used in the two sets of scenario workshops are then described in detail along with the data collected and analysed. The article concludes with some reflections on the use of scenarios in practice as well as an acknowledgment that practice theory would be useful in investigating leadership capability development.