Hybridization Capture Using Short PCR Products Enriches Small Genomes by Capturing Flanking Sequences (CapFlank)

Solution hybridization capture methods utilize biotinylated oligonucleotides as baits to enrich homologous sequences from next generation sequencing (NGS) libraries. Coupled with NGS, the method generates kilo to gigabases of high confidence consensus targeted sequence. However, in many experiments, a non-negligible fraction of the resulting sequence reads are not homologous to the bait. We demonstrate that during capture, the bait-hybridized library molecules add additional flanking library sequences iteratively, such that baits limited to targeting relatively short regions (e.g. few hundred nucleotides) can result in enrichment across entire mitochondrial and bacterial genomes. Our findings suggest that some of the off-target sequences derived in capture experiments are non-randomly enriched, and that CapFlank will facilitate targeted enrichment of large contiguous sequences with minimal prior target sequence information. (Résumé d'auteur

Three caveats that will change our design culture

The article examines how mining culture will be forced to evolve again at a much more fundamental level. Over the past 30 years, the average grade of Australian ore bodies being mined has halved while the waste removed to access the minerals has more than doubled. The energy cost of mining represents approximately seven per cent of Australian energy consumption. In the past eight years Australian mines incurred a 70 per cent rise in energy use, and a 24 per cent decline in productivity over the same period. The cost of electricity in Australia is predicted to increase over the next few years for both domestic and industrial consumers. Most of the electricity used in Australia is generated using coal as a fuel. Understanding when global oil production may peak is relevant to heavy industries and related markets. The IEA is a Paris-based autonomous intergovernmental organization that was established in the wake of the 1973 oil crisis, in the framework of the Organization for Economic Co-operation and Development (OECD)

Approximation of surface area of fines in blast induced fragmentation

The surface area of fragmentation, especially in the finer size fractions, is a useful property to characterise the mechanisms of rock breakage. In the past, researchers have made assumptions with regard to the shape of fragments in order to estimate surface area, such as that all fragments are the same shape or all fragments are spheres. Often these assumptions were developed with inappropriate measures and returned considerable variability and error for the calculation of surface area. This paper reports a model to estimate fragmentation surface area from sieve sized raw data and a density measurement, with experimental validation down to a size fraction of –45 + 38 μm in a range of rock types. After characterisation of particle shape, a range of fragment shapes was found to be in each size fraction. Nevertheless, in the √2 sieve series the average fragment mass, volume and the size fraction standard deviations could be predicted reasonably accurately. Ellipsoid geometry was used to describe particle shape. Using these parameters and the number of fragments (also predicted) in each sieve size the individual surface area of each fragment was simulated

Importance of strain to fragment strength in blasting induced pre-conditioning

When a rock is blasted, cracks propagate through the rock causing the rock to fracture. This paper focuses on applying the results from a series of small scale blasting tests were designed to show the effect that varying blast variables such as explosive type and explosive energy have on the resulting strength of the post blast fragments. It was shown that the velocity of detonation of the explosive product affects the reduction of fragment strength. This has important implications for the downstream comminution process. The observations from these tests are then explained with reference to the principles of fracture mechanics. A simple but effective prediction of blast induced preconditioning is shown

Development of new comminution testing methodologies for geometallurgical mapping of ore hardness and throughput

The emerging discipline of ‘geometallurgy’ is becoming increasingly recognised as a discrete and high-value activity that reflects an ongoing trend towards more effective mine site integration and optimisation. Constrained sampling that reflects and defines inherent ore body variability is a key geometallurgical requirement. This requires use of larger numbers of low-cost physical testing which can be applied to small sample volumes suitable for defining natural variability. The AMIRA P843 ‘GeMIII’ project (Geometallurgical Mapping and Mine Modelling) is a major industry-supported research initiative designed to develop new tools, methods and protocols to support geometallurgical integration. As part of this integrated research a new more rapid low-cost comminution test (GeM Comminution index) has been developed which can be employed as a front line tool for geometallurgical mapping purposes and predictive throughput modelling. The test has been designed to be inserted into routine assay sample preparation and is based on constrained jaw crushing protocols linked to analysis of resultant size distributions. Extensive validation and modelling has shown the GeM Comminution Index (Ci) is correlated with the Drop Weight index A*b and Bond Mill Work Index (BMWi). Large scale trials have been conducted within a commercial assay laboratory to demonstrate and optimise incorporation of the Ci test into routine sample preparation protocols. While Ci based estimates of A*b and BMWi are not as precise compared to larger volume more expensive test-work, the ability to undertake large numbers of tests typically in a systematic downhole manner, provides a high level of data support through adjacency. A Ci based approach is highly suitable for variability mapping, domaining and selecting large composite samples for more precise testing. Within the context of the AMIRA P843 project this forms part of an integrated work fl ow designed to support geometallurgical integration. The development of a comminution test linked to routine assay sample preparation represents significant value adding to a process that in most cases is already going to be carried out. This paper introduces the Ci test concept and application to geometallurgical testing for throughput modelling

REPRISES PLIO-PLEISTOCENES DU PALEOKARST QUERCINOIS

National audienceL'investigation du paléokarst du Sud-Quercy (France) a révélé en de nombreux points une reprise d'érosion et remblaiement superficiels de la plateforme karstique jurassique, succédant à celle plus généralisée du Paléogène. Cette reprise est marquée par la présence de fossiles, notamment de grands et petits mammifères. La note dresse un inventaire de ces localités dans leur contexte géologique et de leurs restes fossiles. Leurs âges sont distribués depuis le Pliocène supérieur jusqu'à l'Holocène et principalement dans la période du Pléistocène moyen et supérieur (de 0,5 à 0,1 Ma)

REPRISES PLIO-PLEISTOCENES DU PALEOKARST QUERCINOIS

National audienceL'investigation du paléokarst du Sud-Quercy (France) a révélé en de nombreux points une reprise d'érosion et remblaiement superficiels de la plateforme karstique jurassique, succédant à celle plus généralisée du Paléogène. Cette reprise est marquée par la présence de fossiles, notamment de grands et petits mammifères. La note dresse un inventaire de ces localités dans leur contexte géologique et de leurs restes fossiles. Leurs âges sont distribués depuis le Pliocène supérieur jusqu'à l'Holocène et principalement dans la période du Pléistocène moyen et supérieur (de 0,5 à 0,1 Ma)

Testing the effects of homology on CapFlank.

<p>Non-homologous amplicon libraries with or without M13 adaptors added (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109101#pone.0109101.s001" target="_blank">Figure S1</a>) representing a potato blight PiRXLRc, giant squid mtDNA ND4, pigeon mtDNA COI, and grape chlorplast rbcL sequences were captured with blight panel A or pigeon panel B 200 bp baits. The capture libraries were then analysed by qPCR for the 250 bp amplicon products for each of the 4 amplicons. Captured libraries without M13 adaptors are shown in blue and with M13 adaptors added shown in red and demonstrate an increase in enrichment with M13 adaptor addition.</p