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.     

Communication arising. Is coral bleaching really adaptive?

From an experiment in which corals are transplanted between two depths on a Panamanian coral reef, Baker infers that bleaching may sometimes help reef corals to survive environmental change. Although Baker's results hint at further mechanisms by which reef-building corals may acclimatize to changing light conditions, we do not consider that the evidence supports his inference.     

PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes

DNA microarrays can be used to identify gene expression changes characteristic of human disease. This is challenging, however, when relevant differences are subtle at the level of individual genes. We introduce an analytical strategy, Gene Set Enrichment Analysis, designed to detect modest but coordinate changes in the expression of groups of functionally related genes. Using this approach, we identify a set of genes involved in oxidative phosphorylation whose expression is coordinately decreased in human diabetic muscle. Expression of these genes is high at sites of insulin-mediated glucose disposal, activated by PGC-1alpha and correlated with total-body aerobic capacity. Our results associate this gene set with clinically important variation in human metabolism and illustrate the value of pathway relationships in the analysis of genomic profiling experiments.     

On the Usefulness of the Ackoff–Gharajedaghi Model of System Types for the Design of Business Systems

The Ackoff–Gharajedaghi Model of System Types distinguishes 3 fundamental empirical systems: deterministic, animate, and social, with regard to their purpose. It has been formulated as a meta-model to support understanding, selection, and formulation of management models and theories. It is argued here that this model is also valuable for the interpretation and design of actual, empirical business systems. A study of a malfunctioning business is presented and interpreted with the Ackoff–Gharajedaghi Model, which supports this argument. Additionally, the study shows a pragmatic value of the proposed Imperative of Goals Alignment for the design of business systems, which is an operationalization of the Ackoff–Gharajedaghi Model. Furthermore, the investigation illustrates the importance of clear goals and incentives in business design; and it supports the thesis of the Ackoff–Gharajedaghi Model that management models and theories, founded upon empirical observations of deterministic and animate systems, impose limitations on the design of business systems.     

Non-collinear states in magnetic sensors

Certain materials have an electrical conductivity that is extremely sensitive to an applied magnetic field; this phenomenon, termed 'giant magnetoresistance', can be used in sensor applications. Typically, such a device comprises several ferromagnetic layers, separated by non-magnetic spacer layer(s)--a so-called 'super-lattice' geometry. In the absence of a magnetic field, the ferromagnetic layers may be magnetized in opposite directions by interlayer exchange coupling, while an applied external magnetic field causes the magnetization directions to become parallel. Because the resistivity depends on the magnetization direction, an applied field that changes the magnetic configuration may be detected simply by measuring the change in resistance. In order to detect weak fields, the energy difference between different magnetization directions should be small; this is usually achieved by using many non-magnetic atomic spacer layers. Here we show, using first-principles theory, that materials combinations such as Fe/V/Co multilayers can produce a non-collinear magnetic state in which the magnetization direction between Fe and Co layers differs by about 90 degrees. This state is energetically almost degenerate with the collinear magnetic states, even though the number of non-magnetic vanadium spacer layers is quite small.     

Common variants at 12q15 and 12q24 are associated with infant head circumference

To identify genetic variants associated with head circumference in infancy, we performed a meta-analysis of seven genome-wide association studies (GWAS) (N = 10,768 individuals of European ancestry enrolled in pregnancy and/or birth cohorts) and followed up three lead signals in six replication studies (combined N = 19,089). rs7980687 on chromosome 12q24 (P = 8.1 × 10(-9)) and rs1042725 on chromosome 12q15 (P = 2.8 × 10(-10)) were robustly associated with head circumference in infancy. Although these loci have previously been associated with adult height, their effects on infant head circumference were largely independent of height (P = 3.8 × 10(-7) for rs7980687 and P = 1.3 × 10(-7) for rs1042725 after adjustment for infant height). A third signal, rs11655470 on chromosome 17q21, showed suggestive evidence of association with head circumference (P = 3.9 × 10(-6)). SNPs correlated to the 17q21 signal have shown genome-wide association with adult intracranial volume, Parkinson's disease and other neurodegenerative diseases, indicating that a common genetic variant in this region might link early brain growth with neurological disease in later life.     

Embracing the quantum limit in silicon computing

Quantum computers hold the promise of massive performance enhancements across a range of applications, from cryptography and databases to revolutionary scientific simulation tools. Such computers would make use of the same quantum mechanical phenomena that pose limitations on the continued shrinking of conventional information processing devices. Many of the key requirements for quantum computing differ markedly from those of conventional computers. However, silicon, which plays a central part in conventional information processing, has many properties that make it a superb platform around which to build a quantum computer.