Structure of a protein determined by solid-state magic-angle-spinning NMR spectroscopy

The determination of a representative set of protein structures is a chief aim in structural genomics. Solid-state NMR may have a crucial role in structural investigations of those proteins that do not easily form crystals or are not accessible to solution NMR, such as amyloid systems or membrane proteins. Here we present a protein structure determined by solid-state magic-angle-spinning (MAS) NMR. Almost complete (13)C and (15)N resonance assignments for a micro-crystalline preparation of the alpha-spectrin Src-homology 3 (SH3) domain formed the basis for the extraction of a set of distance restraints. These restraints were derived from proton-driven spin diffusion (PDSD) spectra of biosynthetically site-directed, labelled samples obtained from bacteria grown using [1,3-(13)C]glycerol or [2-(13)C]glycerol as carbon sources. This allowed the observation of long-range distance correlations up to approximately 7 A. The calculated global fold of the alpha-spectrin SH3 domain is based on 286 inter-residue (13)C-(13)C and six (15)N-(15)N restraints, all self-consistently obtained by solid-state MAS NMR. This MAS NMR procedure should be widely applicable to small membrane proteins that can be expressed in bacteria.     

Vegetation changes after livestock grazing exclusion and shrub control in the southern Chihuahuan Desert

Vegetation cover and production were evaluated after nearly 7 years of livestock grazing exclusion and shrub control in an area with a long history of heavy livestock grazing in the southern Chihuahuan Desert, Mexico. An exclosure was established to prevent livestock grazing. In half of the excluded area, the main shrub, Larrea tridentata , was mechanically controlled. Outside the exclosure, heavy livestock grazing occurred as customary and shrubs were not controlled. Absence of grazing resulted in 50% higher grass cover and 35% higher total biomass. Larrea tridentata cover was twice as high on the grazed area as on the ungrazed area. Vegetation cover was dominated by grasses (42%) in the ungrazed area, whereas in the grazed area, cover was equally divided between grasses (28%) and shrubs (27%). Shrub control did not affect vegetation cover or herbage production. Multivariate analysis confirmed that inside the excluded area, shrub control had little impact on the plant community. The effect of grazing, however, clearly distinguished the community outside the exclosure from that inside the exclosure.     

De novo assembly and genotyping of variants using colored de Bruijn graphs

Detecting genetic variants that are highly divergent from a reference sequence remains a major challenge in genome sequencing. We introduce de novo assembly algorithms using colored de Bruijn graphs for detecting and genotyping simple and complex genetic variants in an individual or population. We provide an efficient software implementation, Cortex, the first de novo assembler capable of assembling multiple eukaryotic genomes simultaneously. Four applications of Cortex are presented. First, we detect and validate both simple and complex structural variations in a high-coverage human genome. Second, we identify more than 3 Mb of sequence absent from the human reference genome, in pooled low-coverage population sequence data from the 1000 Genomes Project. Third, we show how population information from ten chimpanzees enables accurate variant calls without a reference sequence. Last, we estimate classical human leukocyte antigen (HLA) genotypes at HLA-B, the most variable gene in the human genome.     

Evaluating Scientific Research Projects: The Units of Science in the Making

Original research is of course what scientists are expected to do. Therefore the research project is in many ways the unit of science in the making: it is the center of the professional life of the individual scientist and his coworkers. It is also the means towards the culmination of their specific activities: the original publication they hope to contribute to the scientific literature. The scientific project should therefore be of central interest to all the students of science, particularly the philosophers and sociologists of science. We shall focus on the preliminary evaluation of research projects—the specific task of referees—and will emphasize the problem of their scientificity—the chief concern of scientific gatekeepers. In the past such an examination aimed only at protecting the taxpayer from swindlers and incompetent amateurs, such as the inventors of continuous motion artifacts. In recent times a similar issue has resurfaced with regard to some of the most prestigious and most handsomely funded projects, namely work on string theory and many-worlds cosmology. Indeed, some of their faithful have claimed that these theories are so elegant, and so full of high-grade mathematics, that they should be exempted from empirical tests. This claim provoked the spirited rebuttal of the well-known cosmologists Ellis and Silk (Nature 516:321–323, 2014), which the present paper is intended to reinforce. Indeed, we shall try to show why empirical testability is necessary though insufficient for a piece of work to qualify as scientific. Finally, the present paper may also be regarded as an indirect contribution to the current debate over the reliability of quantitative indicators of scientific worth, such as the h-index of scientific productivity (e.g., Wilsdon in Nature 523:129, 2015). But we shall touch only tangentially on the sociological, political, and economics of research teams: our focus will be the acquisition of new scientific knowledge.     

Roosting behavior of the Mexican free-tailed bat ( Tadarida brasiliensis ) in a highway overpass

A colony of Mexican free-tailed bats ( Tadarida brasiliensis ) roosting in an interstate highway overpass in Belton, Bell County, Texas, was studied weekly from 28 June to 21 November 1996 (except for the week of 4 July). We examined 2 aspects of roosting behavior: site-specific fidelity to locations within the roost and gender-related segregation within the roost. Colony estimates based on guano production showed a marked decrease in the number of bats from 19 to 26 July; many of these departing bats were adult females. No female bats sampled after this interval were pregnant. Male bats outnumbered females on nearly all sampling occasions. Throughout the study, one section of the roost was dominated by males, ranging from 83% to 100% of total bats. The majority of bats recaptured at least once were faithful to specific locations within the roost, and more than 70% of bats recaptured multiple times were faithful to specific roost locations.     

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes ( approximately 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.     

Electronic read-out of a single nuclear spin using a molecular spin transistor

Quantum control of individual spins in condensed-matter devices is an emerging field with a wide range of applications, from nanospintronics to quantum computing. The electron, possessing spin and orbital degrees of freedom, is conventionally used as the carrier of quantum information in proposed devices. However, electrons couple strongly to the environment, and so have very short relaxation and coherence times. It is therefore extremely difficult to achieve quantum coherence and stable entanglement of electron spins. Alternative concepts propose nuclear spins as the building blocks for quantum computing, because such spins are extremely well isolated from the environment and less prone to decoherence. However, weak coupling comes at a price: it remains challenging to address and manipulate individual nuclear spins. Here we show that the nuclear spin of an individual metal atom embedded in a single-molecule magnet can be read out electronically. The observed long lifetimes (tens of seconds) and relaxation characteristics of nuclear spin at the single-atom scale open the way to a completely new world of devices in which quantum logic may be implemented.