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.     

Two ten-billion-solar-mass black holes at the centres of giant elliptical galaxies

Observational work conducted over the past few decades indicates that all massive galaxies have supermassive black holes at their centres. Although the luminosities and brightness fluctuations of quasars in the early Universe suggest that some were powered by black holes with masses greater than 10 billion solar masses, the remnants of these objects have not been found in the nearby Universe. The giant elliptical galaxy Messier 87 hosts the hitherto most massive known black hole, which has a mass of 6.3 billion solar masses. Here we report that NGC 3842, the brightest galaxy in a cluster at a distance from Earth of 98 megaparsecs, has a central black hole with a mass of 9.7 billion solar masses, and that a black hole of comparable or greater mass is present in NGC 4889, the brightest galaxy in the Coma cluster (at a distance of 103 megaparsecs). These two black holes are significantly more massive than predicted by linearly extrapolating the widely used correlations between black-hole mass and the stellar velocity dispersion or bulge luminosity of the host galaxy. Although these correlations remain useful for predicting black-hole masses in less massive elliptical galaxies, our measurements suggest that different evolutionary processes influence the growth of the largest galaxies and their black holes.     

Overcoming lability of extremely long alkane carbon-carbon bonds through dispersion forces

Steric effects in chemistry are a consequence of the space required to accommodate the atoms and groups within a molecule, and are often thought to be dominated by repulsive forces arising from overlapping electron densities (Pauli repulsion). An appreciation of attractive interactions such as van der Waals forces (which include London dispersion forces) is necessary to understand chemical bonding and reactivity fully. This is evident from, for example, the strongly debated origin of the higher stability of branched alkanes relative to linear alkanes and the possibility of constructing hydrocarbons with extraordinarily long C-C single bonds through steric crowding. Although empirical bond distance/bond strength relationships have been established for C-C bonds (longer C-C bonds have smaller bond dissociation energies), these have no present theoretical basis. Nevertheless, these empirical considerations are fundamental to structural and energetic evaluations in chemistry, as summarized by Pauling as early as 1960 and confirmed more recently. Here we report the preparation of hydrocarbons with extremely long C-C bonds (up to 1.704??), the longest such bonds observed so far in alkanes. The prepared compounds are unexpectedly stable--noticeable decomposition occurs only above 200?°C. We prepared the alkanes by coupling nanometre-sized, diamond-like, highly rigid structures known as diamondoids. The extraordinary stability of the coupling products is due to overall attractive dispersion interactions between the intramolecular H???H contact surfaces, as is evident from density functional theory computations with and without inclusion of dispersion corrections.     

Experimental infection of bats with Geomyces destructans causes white-nose syndrome

White-nose syndrome (WNS) has caused recent catastrophic declines among multiple species of bats in eastern North America. The disease's name derives from a visually apparent white growth of the newly discovered fungus Geomyces destructans on the skin (including the muzzle) of hibernating bats. Colonization of skin by this fungus is associated with characteristic cutaneous lesions that are the only consistent pathological finding related to WNS. However, the role of G. destructans in WNS remains controversial because evidence to implicate the fungus as the primary cause of this disease is lacking. The debate is fuelled, in part, by the assumption that fungal infections in mammals are most commonly associated with immune system dysfunction. Additionally, the recent discovery that G. destructans commonly colonizes the skin of bats of Europe, where no unusual bat mortality events have been reported, has generated further speculation that the fungus is an opportunistic pathogen and that other unidentified factors are the primary cause of WNS. Here we demonstrate that exposure of healthy little brown bats (Myotis lucifugus) to pure cultures of G. destructans causes WNS. Live G. destructans was subsequently cultured from diseased bats, successfully fulfilling established criteria for the determination of G. destructans as a primary pathogen. We also confirmed that WNS can be transmitted from infected bats to healthy bats through direct contact. Our results provide the first direct evidence that G. destructans is the causal agent of WNS and that the recent emergence of WNS in North America may represent translocation of the fungus to a region with a naive population of animals. Demonstration of causality is an instrumental step in elucidating the pathogenesis and epidemiology of WNS and in guiding management actions to preserve bat populations against the novel threat posed by this devastating infectious disease.     

Synthesis of ferrocenyl-1,2-diketones and related compounds: Crystal and molecular structures of 1,2-diferrocenylethanedione and 1-ferrocenyl-2-(4-biphenylyl) ethanedione

Ferrocenyl-1,2-diketones FcCOCOR, 3, [Fc = (C₅H₅)Fe(C₅H₄)] can be prepared by oxidation of acylferrocenes FcCOCH₂R or, more efficiently, by oxidation of the isomeric ketones FcCH₂COR, 2. The ketones 2 are in turn readily synthesized from the salt (FcCH₂PPh₃)⁺I⁻ via the acylated salts [FcCH(COR)PPh₃]⁺I⁻. The haloacylferocenes FcCOCCl_x H_3−x (x = 1, 2, 3, of which the x = 2 example is synthetically equivalent to a diketone) are synthesized by Friedel—Crafts acylation of ferrocene using CCl_xH_3−xCOCl/AlCl₃, but the reaction proceeds via two parallel pathways, one giving the normal acyl derivatives FcCOCCl_xH_3−x and the other giving the reduced products FcCOCCl_x−1H_4−x. Two diketones FcCOCOFc 3b and FcCOCOC₆H₄Ph 3c have been structurally characterised by single-crystal X-ray diffraction.     

In Vivo Endoscopic Tissue Identification by Rapid Evaporative Ionization Mass Spectrometry (REIMS)

Gastrointestinal cancers are a leading cause of mortality, accounting for 23 % of cancer‐related deaths worldwide. In order to improve outcomes from these cancers, novel tissue characterization methods are needed to facilitate accurate diagnosis. Rapid evaporative ionization mass spectrometry (REIMS) is a technique developed for the in vivo classification of human tissue through mass spectrometric analysis of aerosols released during electrosurgical dissection. This ionization technique was further developed by utilizing surface induced dissociation and was integrated with an endoscopic polypectomy snare to allow in vivo analysis of the gastrointestinal tract. We tested the classification performance of this novel endoscopic REIMS method in vivo. It was shown to be capable of differentiating between healthy layers of the intestinal wall, cancer, and adenomatous polyps based on the REIMS fingerprint of each tissue type in vivo.     

Comparison of phantom materials for use in quality assurance of microbeam radiation therapy

Microbeam radiation therapy (MRT) is a promising radiotherapy modality that uses arrays of spatially fractionated micrometre‐sized beams of synchrotron radiation to irradiate tumours. Routine dosimetry quality assurance (QA) prior to treatment is necessary to identify any changes in beam condition from the treatment plan, and is undertaken using solid homogeneous phantoms. Solid phantoms are designed for, and routinely used in, megavoltage X‐ray beam radiation therapy. These solid phantoms are not necessarily designed to be water‐equivalent at low X‐ray energies, and therefore may not be suitable for MRT QA. This work quantitatively determines the most appropriate solid phantom to use in dosimetric MRT QA. Simulated dose profiles of various phantom materials were compared with those calculated in water under the same conditions. The phantoms under consideration were RMI457 Solid Water (Gammex‐RMI, Middleton, WI, USA), Plastic Water (CIRS, Norfolk, VA, USA), Plastic Water DT (CIRS, Norfolk, VA, USA), PAGAT (CIRS, Norfolk, VA, USA), RW3 Solid Phantom (PTW Freiburg, Freiburg, Germany), PMMA, Virtual Water (Med‐Cal, Verona, WI, USA) and Perspex. RMI457 Solid Water and Virtual Water were found to be the best approximations for water in MRT dosimetry (within ±3% deviation in peak and 6% in valley). RW3 and Plastic Water DT approximate the relative dose distribution in water (within ±3% deviation in the peak and 5% in the valley). PAGAT, PMMA, Perspex and Plastic Water are not recommended to be used as phantoms for MRT QA, due to dosimetric discrepancies greater than 5%.     

Adsorption and diffusion of argon in disordered nanoporous carbons

Application-specific optimization of disordered nanoporous carbons remains a formidable challenge due to the difficulty in accurately characterizing their microstructures with current empirical methods. Using molecular simulation techniques, we investigated the adsorptive and diffusive behavior of argon in three models of disordered nanoporous carbons. We found that the structural and morphological differences between these models gave rise to distinct phenomenological properties. The adsorptive behavior of argon in both the low and high pressure regimes was enhanced dramatically in the models with more crystalline microstructures. As for dynamic properties, we found that the adsorbent’s structure and energetic topology significantly alters the rates of diffusion as well as the characteristics of the underlying diffusion mechanisms.