An integrated semiconductor device enabling non-optical genome sequencing

The seminal importance of DNA sequencing to the life sciences, biotechnology and medicine has driven the search for more scalable and lower-cost solutions. Here we describe a DNA sequencing technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical DNA sequencing of genomes. Sequence data are obtained by directly sensing the ions produced by template-directed DNA polymerase synthesis using all-natural nucleotides on this massively parallel semiconductor-sensing device or ion chip. The ion chip contains ion-sensitive, field-effect transistor-based sensors in perfect register with 1.2 million wells, which provide confinement and allow parallel, simultaneous detection of independent sequencing reactions. Use of the most widely used technology for constructing integrated circuits, the complementary metal-oxide semiconductor (CMOS) process, allows for low-cost, large-scale production and scaling of the device to higher densities and larger array sizes. We show the performance of the system by sequencing three bacterial genomes, its robustness and scalability by producing ion chips with up to 10 times as many sensors and sequencing a human genome.     

Year-round activity patterns in a hyperdiverse community of rainforest amphibians in Madagascar

Madagascar hosts a high diversity of amphibians estimated at over 500 species, nearly all of them endemic. Surprisingly few data are available on the activity cycles of this fauna, despite its importance for ecological, evolutionary and conservation research. Here we report the results of a year-round survey of amphibians along a transect bordering the Analamazaotra forest near Andasibe in central eastern Madagascar. During 120 transect walks evenly spaced through the year, a total of 2530 individuals of 40 species of anurans was observed. Abundance was higher during the warm/rainy season (December to April) and peaked in February. Of the five climatic predictors measured, only mean temperature and relative humidity showed high importance values, and multi-model averages indicate that these two variables have a strong effect on amphibian abundance along the transect. Species richness showed no evident peak during the study period and was best explained by a model including average temperature and rainfall. Canonical correspondence analysis indicates that Boophis sibilans, B. tephraeomystax, B. boehmei and Plethodontohyla notosticta were more frequently encountered along the transect on cold and humid days while Plethodontohyla mihanika, Gephyromantis boulengeri and Spinomantis aglavei were distinctly more abundant on cold and dry days, and Paradoxophyla palmata on warm and dry days. The results of our study flag a number of species as suitable candidates for future monitoring initiatives and suggest that a simple combination of visual and acoustic surveys can estimate amphibian activity with high sample sizes in Madagascar’s rainforests.     

Pragmatic Holism (or pragmatic reductionism)

The reductionist/holist debate is highly polarised. I propose an intermediate position of pragmatic holism. It derives from two claims: firstly, that irrespective of whether all natural systems are theoretically reducible, for many systems it is utterly impractical to attempt such a reduction, and secondly, that regardless of whether irreducible 'wholes exist, it is vain to try and prove this. This position illuminates the debate along new pragmatic lines by refocussing attention on the underlying heuristics of learning about the natural world.     

Dimethyloxarsylethanol from anaerobic decomposition of brown kelp (Ecklonia radiata): A likely precursor of arsenobetaine in marine fauna

Summary The novel arsenic compound, dimethyloxarsylethanol, has been isolated from anaerobically incubatedEcklonia radiata. It is proposed that this compound has a key position in the biosynthesis of arsenobetaine.C, H microanalyses were performed by the Australian Microanalytical Service.     

Discovery of abundant hydrothermal venting on the ultraslow-spreading Gakkel ridge in the Arctic Ocean

Submarine hydrothermal venting along mid-ocean ridges is an important contributor to ridge thermal structure, and the global distribution of such vents has implications for heat and mass fluxes from the Earth's crust and mantle and for the biogeography of vent-endemic organisms. Previous studies have predicted that the incidence of hydrothermal venting would be extremely low on ultraslow-spreading ridges (ridges with full spreading rates <2 cm x yr(-1)-which make up 25 per cent of the global ridge length), and that such vent systems would be hosted in ultramafic in addition to volcanic rocks. Here we present evidence for active hydrothermal venting on the Gakkel ridge, which is the slowest spreading (0.6-1.3 cm x yr(-1)) and least explored mid-ocean ridge. On the basis of water column profiles of light scattering, temperature and manganese concentration along 1,100 km of the rift valley, we identify hydrothermal plumes dispersing from at least nine to twelve discrete vent sites. Our discovery of such abundant venting, and its apparent localization near volcanic centres, requires a reassessment of the geologic conditions that control hydrothermal circulation on ultraslow-spreading ridges.     

Periodicity in fish otolith Sr,Na, and K corresponds with visual banding

Examination of a section of an otolith from a teleost fish by fast atom bombardment-secondary ion mass spectrometry (FAB-SIMS) revealed seasonal periodicity in Sr, Na, and K concentrations that corresponded with visually observed annual banding. Strontium maxima also corresponded with Na and K minima and vice versa. In addition there was a general, apparently age-related, trend in Sr levels, with concentrations at the edge of the otolith being higher than in the core.     

Glycerylphosphorylarsenocholine and phosphatidylarsenocholine in yelloweye mullet (Aldrichetta forsteri) following oral administration of arsenocholine

Summary The novel arsenical glycerylphosphorylarsenocholine has been isolated from yelloweye mullet (Aldrichetta forsteri) following oral administration of arsenocholine. Ether-soluble arsenic was shown to be present as phosphatidylarsenocholine.