The genome sequence of Atlantic cod reveals a unique immune system

Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that sustains long-standing commercial fisheries and incipient aquaculture. Here we present the genome sequence of Atlantic cod, showing evidence for complex thermal adaptations in its haemoglobin gene cluster and an unusual immune architecture compared to other sequenced vertebrates. The genome assembly was obtained exclusively by 454 sequencing of shotgun and paired-end libraries, and automated annotation identified 22,154 genes. The major histocompatibility complex (MHC)?II is a conserved feature of the adaptive immune system of jawed vertebrates, but we show that Atlantic cod has lost the genes for MHC?II, CD4 and invariant chain (Ii) that are essential for the function of this pathway. Nevertheless, Atlantic cod is not exceptionally susceptible to disease under natural conditions. We find a highly expanded number of MHC?I genes and a unique composition of its Toll-like receptor (TLR) families. This indicates how the Atlantic cod immune system has evolved compensatory mechanisms in both adaptive and innate immunity in the absence of MHC?II. These observations affect fundamental assumptions about the evolution of the adaptive immune system and its components in vertebrates.     

Measurement of the internal state of a single atom without energy exchange

A measurement necessarily changes the quantum state being measured, a phenomenon known as back-action. Real measurements, however, almost always cause a much stronger back-action than is required by the laws of quantum mechanics. Quantum non-demolition measurements have been devised that keep the additional back-action entirely within observables other than the one being measured. However, this back-action on other observables often imposes its own constraints. In particular, free-space optical detection methods for single atoms and ions (such as the shelving technique, a sensitive and well-developed method) inevitably require spontaneous scattering, even in the dispersive regime. This causes irreversible energy exchange (heating), which is a limitation in atom-based quantum information processing, where it obviates straightforward reuse of the qubit. No such energy exchange is required by quantum mechanics. Here we experimentally demonstrate optical detection of an atomic qubit with significantly less than one spontaneous scattering event. We measure the transmission and reflection of an optical cavity containing the atom. In addition to the qubit detection itself, we quantitatively measure how much spontaneous scattering has occurred. This allows us to relate the information gained to the amount of spontaneous emission, and we obtain a detection error below 10 per cent while scattering less than 0.2 photons on average. Furthermore, we perform a quantum Zeno-type experiment to quantify the measurement back-action, and find that every incident photon leads to an almost complete state collapse. Together, these results constitute a full experimental characterization of a quantum measurement in the 'energy exchange-free' regime below a single spontaneous emission event. Besides its fundamental interest, this approach could significantly simplify proposed neutral-atom quantum computation schemes, and may enable sensitive detection of molecules and atoms lacking closed transitions.     

Structure and function of an irreversible agonist-β(2) adrenoceptor complex

G-protein-coupled receptors (GPCRs) are eukaryotic integral membrane proteins that modulate biological function by initiating cellular signalling in response to chemically diverse agonists. Despite recent progress in the structural biology of GPCRs, the molecular basis for agonist binding and allosteric modulation of these proteins is poorly understood. Structural knowledge of agonist-bound states is essential for deciphering the mechanism of receptor activation, and for structure-guided design and optimization of ligands. However, the crystallization of agonist-bound GPCRs has been hampered by modest affinities and rapid off-rates of available agonists. Using the inactive structure of the human β(2) adrenergic receptor (β(2)AR) as a guide, we designed a β(2)AR agonist that can be covalently tethered to a specific site on the receptor through a disulphide bond. The covalent β(2)AR-agonist complex forms efficiently, and is capable of activating a heterotrimeric G protein. We crystallized a covalent agonist-bound β(2)AR-T4L fusion protein in lipid bilayers through the use of the lipidic mesophase method, and determined its structure at 3.5?? resolution. A comparison to the inactive structure and an antibody-stabilized active structure (companion paper) shows how binding events at both the extracellular and intracellular surfaces are required to stabilize an active conformation of the receptor. The structures are in agreement with long-timescale (up to 30?μs) molecular dynamics simulations showing that an agonist-bound active conformation spontaneously relaxes to an inactive-like conformation in the absence of a G protein or stabilizing antibody.     

The earliest evidence for anatomically modern humans in northwestern Europe

The earliest anatomically modern humans in Europe are thought to have appeared around 43,000-42,000 calendar years before present (43-42 kyr cal BP), by association with Aurignacian sites and lithic assemblages assumed to have been made by modern humans rather than by Neanderthals. However, the actual physical evidence for modern humans is extremely rare, and direct dates reach no farther back than about 41-39 kyr cal BP, leaving a gap. Here we show, using stratigraphic, chronological and archaeological data, that a fragment of human maxilla from the Kent's Cavern site, UK, dates to the earlier period. The maxilla (KC4), which was excavated in 1927, was initially diagnosed as Upper Palaeolithic modern human. In 1989, it was directly radiocarbon dated by accelerator mass spectrometry to 36.4-34.7 kyr cal BP. Using a Bayesian analysis of new ultrafiltered bone collagen dates in an ordered stratigraphic sequence at the site, we show that this date is a considerable underestimate. Instead, KC4 dates to 44.2-41.5 kyr cal BP. This makes it older than any other equivalently dated modern human specimen and directly contemporary with the latest European Neanderthals, thus making its taxonomic attribution crucial. We also show that in 13 dental traits KC4 possesses modern human rather than Neanderthal characteristics; three other traits show Neanderthal affinities and a further seven are ambiguous. KC4 therefore represents the oldest known anatomically modern human fossil in northwestern Europe, fills a key gap between the earliest dated Aurignacian remains and the earliest human skeletal remains, and demonstrates the wide and rapid dispersal of early modern humans across Europe more than 40 kyr ago.     

Using sampling and inverse distance weighted modeling for mapping invasive plants

Accurate time- and cost-efficient mapping is central to successful rangeland invasive plant management. In this study sampling together with Inverse Distance Weighted (IDW) interpolation modeling was tested as a mapping alternative to expensive full-coverage delineation survey mapping methods. Our objective was to examine accuracies of presence/absence maps generated from 18 sampling strategies (3 sampling methods × 6 sample densities) using IDW. Invasive plant field survey maps with known accuracies were used to generate samples and to test interpolation results at 2 sites. Site 1 was approximately 6.0 km 2 , dominated by Russian knapweed ( Acroptilon repens L.). Site 2, an upland area of approximately 13.5 km 2 , was dominated by spotted knapweed ( Centaurea maculosa Lam). Sampling method × sample density combinations were gathered from field survey infestation maps using repeated computer-based sampling methods. IDW modeling was applied to each of the sample data sets. Accuracies of the IDW interpolation results were calculated by re-referencing field survey maps. We determined that sampling at density of 0.25% (about 1 point per ha) using a systematic sampling method was the preferred sampling strategy for both sites. This combination of sampling density and method yielded 85% accurate presence/absence maps. We conclude that sampling combined with IDW interpolation modeling can generate accurate invasive plant maps and is a potential alternative to current delineation survey methods.     

Relationships between Centaurea maculosa and indigenous plant assemblages

Ecological impacts of invasive plants include displacement of indigenous species and declines in species richness and diversity. The objective of this study was to characterize the functional relationship between plant community composition and Centaurea maculosa Lam. (spotted knapweed) within a Festuca idahoensis / Pseudoroegneria spicatum habitat type in Montana. Density, cover, and biomass of all species were collected along a gradient of spotted knapweed cover ranging from 0% to about 100%. Step-down regression was used to determine the relationship among C. maculosa , indigenous species, species richness, and Shannon-Weavers diversity index. Regressions showed that indigenous perennial grass cover, species richness, and species diversity were inversely related to C. maculosa cover. There was no relationship between C. maculosa and indigenous forbs. While this study does not imply a causal relationship, the literature suggests that C. maculosa displaces indigenous species and/or invades areas of reduced indigenous plant cover, low diversity, or low species richness. Knowing levels of indigenous perennial grass cover will help managers predict the outcome of weed management on rangelands that are vulnerable to weed infestation.