Label-free immunodetection with CMOS-compatible semiconducting nanowires

Semiconducting nanowires have the potential to function as highly sensitive and selective sensors for the label-free detection of low concentrations of pathogenic microorganisms. Successful solution-phase nanowire sensing has been demonstrated for ions, small molecules, proteins, DNA and viruses; however, 'bottom-up' nanowires (or similarly configured carbon nanotubes) used for these demonstrations require hybrid fabrication schemes, which result in severe integration issues that have hindered widespread application. Alternative 'top-down' fabrication methods of nanowire-like devices produce disappointing performance because of process-induced material and device degradation. Here we report an approach that uses complementary metal oxide semiconductor (CMOS) field effect transistor compatible technology and hence demonstrate the specific label-free detection of below 100 femtomolar concentrations of antibodies as well as real-time monitoring of the cellular immune response. This approach eliminates the need for hybrid methods and enables system-scale integration of these sensors with signal processing and information systems. Additionally, the ability to monitor antibody binding and sense the cellular immune response in real time with readily available technology should facilitate widespread diagnostic applications.     

Whales originated from aquatic artiodactyls in the Eocene epoch of India

Although the first ten million years of whale evolution are documented by a remarkable series of fossil skeletons, the link to the ancestor of cetaceans has been missing. It was known that whales are related to even-toed ungulates (artiodactyls), but until now no artiodactyls were morphologically close to early whales. Here we show that the Eocene south Asian raoellid artiodactyls are the sister group to whales. The raoellid Indohyus is similar to whales, and unlike other artiodactyls, in the structure of its ears and premolars, in the density of its limb bones and in the stable-oxygen-isotope composition of its teeth. We also show that a major dietary change occurred during the transition from artiodactyls to whales and that raoellids were aquatic waders. This indicates that aquatic life in this lineage occurred before the origin of the order Cetacea.     

Multiple-scale roost habitat comparisons of female Merriam’s Wild Turkeys in the southern Black Hills, South Dakota

Because quantity and quality of roosting habitat can affect Merriam’s Wild Turkey ( Meleagris gallopavo merriami ) distribution, we described habitat characteristics of Merriam’s turkey roost sites in the southern Black Hills of South Dakota. Varying proportions of Merriam’s turkeys in the southern Black Hills depended on supplemental feed from livestock operations during the 2 winters of our study, whereas the remainder wintered in forested habitat away from supplemental feed. We compared characteristics of roost habitat occupied by female turkeys from both groups. We located turkeys with radio-transmitters in the early morning and late evening to find roost sites. Female Merriam’s turkeys in the southern Black Hills roosted exclusively in ponderosa pine trees, primarily on the upper portions of ridges on easterly aspects. Generally, trees >30 cm diameter at breast height (dbh) were chosen for roosting, but turkeys also roosted in trees with smaller dbh. During winter months, turkeys that relied on supplemental feeding roosted adjacent to the ranch-farmstead where the supplemental food was located. Generally, these turkeys used the same roost site(s) throughout the winter, whereas turkeys that remained in the forest during winter used multiple roost sites. We suggest maintaining stands of trees >30 cm dbh on the upper portions of easterly aspects to provide suitable roosting habitat for female Merriam’s Wild Turkeys in the southern Black Hills.     

A framework for variation discovery and genotyping using next-generation DNA sequencing data

Recent advances in sequencing technology make it possible to comprehensively catalog genetic variation in population samples, creating a foundation for understanding human disease, ancestry and evolution. The amounts of raw data produced are prodigious, and many computational steps are required to translate this output into high-quality variant calls. We present a unified analytic framework to discover and genotype variation among multiple samples simultaneously that achieves sensitive and specific results across five sequencing technologies and three distinct, canonical experimental designs. Our process includes (i) initial read mapping; (ii) local realignment around indels; (iii) base quality score recalibration; (iv) SNP discovery and genotyping to find all potential variants; and (v) machine learning to separate true segregating variation from machine artifacts common to next-generation sequencing technologies. We here discuss the application of these tools, instantiated in the Genome Analysis Toolkit, to deep whole-genome, whole-exome capture and multi-sample low-pass (～4×) 1000 Genomes Project datasets.     

The genome of Theobroma cacao

We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example, flavonoid-related genes. It also provides a major source of candidate genes for T. cacao improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions.     

Comparative tolerance of four stocks of cuttthroat trout to extremes in temperature, salinity, and hypoxia

Four stocks of cutthroat trout ( Oncorhynchus clarki ) were exposed to high temperature, high salinity, and low dissolved oxygen to determine inherent differences. The fish tested included 2 stocks of Bonneville cutthroat trout ( O. c. utah ), a lacustrine stock derived from Bear Lake and a fluvial-origin stock from southern Utah (Manning Meadow Reservoir). The other 2 stocks tested were from Electric Lake (largely Yellowstone cutthroat trout, O. c. bouvieri ) and Jackson Hole, Wyoming (fine-spotted Snake River cutthroat trout, O. c. subsp.). Temperature tests were either critical thermal maximum (CTM) or 96-hour trials using juveniles acclimated between 12.5° C and 18.0° C. Two CTM end points were temperature at first loss of equilibrium (CTM eq ) and onset of spasms (CTM s ). There were no significant differences in CTM eq among test fish acclimated to 18.0° C, but CTM s was significantly higher for Bear Lake Bonneville (30.0°C) than for Snake River (29.6° C) or southern Bonneville (29.7° C) stocks. With fish acclimated at 13.0° C, there were no significant differences among the stocks in CTM eq or CTM s . Differences among stocks varied significantly among nine 96-hour tests. Overall, it appeared that the southern Bonneville stock had slightly better survival at warmer temperatures than other stocks. In 24-hour survival tests at high salinities, the Snake River stock had the lowest tolerance, with significant mortality occuring at 18% (29.5 mS · cm -1 conductivity). The southern Bonneville stock had the highest tolerance, with no mortality until 22% (38 mS · cm -1 ). Bear Lake Bonneville and Electric Lake stocks had 60% and 30% mortality, respectively, at 21% (36 mS · cm -1 ). Hypoxia tolerance measured by resistance time, 24-hour mortality, or probit analysis (LEC 50 ) did not differ among stocks. The 24-hour LEC 50 was 2.34 mg O 2 · L -1 for all stocks combined.     

Functional characterisation of naturally occurring mutations in human melanopsin

Melanopsin is a blue light-sensitive opsin photopigment involved in a range of non-image forming behaviours, including circadian photoentrainment and the pupil light response. Many naturally occurring genetic variants exist within the human melanopsin gene (OPN4), yet it remains unclear how these variants affect melanopsin protein function and downstream physiological responses to light. Here, we have used bioinformatic analysis and in vitro expression systems to determine the functional phenotypes of missense human OPN4 variants. From 1242 human OPN4 variants collated in the NCBI Short Genetic Variation database (dbSNP), we identified 96 that lead to non-synonymous amino acid substitutions. These 96 missense mutations were screened using sequence alignment and comparative approaches to select 16 potentially deleterious variants for functional characterisation using calcium imaging of melanopsin-driven light responses in HEK293T cells. We identify several previously uncharacterised OPN4 mutations with altered functional properties, including attenuated or abolished light responses, as well as variants demonstrating abnormal response kinetics. These data provide valuable insight into the structure–function relationships of human melanopsin, including several key functional residues of the melanopsin protein. The identification of melanopsin variants with significantly altered function may serve to detect individuals with disrupted melanopsin-based light perception, and potentially highlight those at increased risk of sleep disturbance, circadian dysfunction, and visual abnormalities.