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.     

Sequence-based characterization of structural variation in the mouse genome

Structural variation is widespread in mammalian genomes and is an important cause of disease, but just how abundant and important structural variants (SVs) are in shaping phenotypic variation remains unclear. Without knowing how many SVs there are, and how they arise, it is difficult to discover what they do. Combining experimental with automated analyses, we identified 711,920 SVs at 281,243 sites in the genomes of thirteen classical and four wild-derived inbred mouse strains. The majority of SVs are less than 1?kilobase in size and 98% are deletions or insertions. The breakpoints of 160,000 SVs were mapped to base pair resolution, allowing us to infer that insertion of retrotransposons causes more than half of SVs. Yet, despite their prevalence, SVs are less likely than other sequence variants to cause gene expression or quantitative phenotypic variation. We identified 24 SVs that disrupt coding exons, acting as rare variants of large effect on gene function. One-third of the genes so affected have immunological functions.     

Behaviour and habitat of Neohela monstrosa (Boeck, 1861) (Amphipoda: Corophiida) in Norwegian Sea deep water

There are few in situ observations of deep-sea macrofauna, due to the remoteness of this ecosystem. Visual surveys conducted for marine management by MAREANO, (marine area database for Norwegian waters) and the petroleum industry (by SERPENTS, scientific and environmental remotely operated vehicle partnership using existing industrial technology) have provided unique material of visual information from large areas in the Norwegian Sea. The distribution, density and behaviour of the deep-sea amphipod Neohela monstrosa (Boeck, 1861) is described based on videos and samples from the Norwegian Sea. This amphipod is common on mud bottoms at 200–2181 m depth in the area. Dense communities were found in stands of the arctic sea pen Umbellula encrinus at more than 1000 m depth where temperatures were below 0° C. The mean density of N. monstrosa observed for larger areas was 4/100 m² but densities of 15–36 individuals per m² were found in local patches. It is domicolous which is characteristic of the superfamily Corophiida and digs burrows in soft muddy bottoms primarily by using large shovel-like gnathopods to scoop the sediment out. The amphipod was observed pushing and rolling sediment balls out of its burrow, which were probably held together with amphipod silk. It digs out an upper 3 to 4 cm wide burrow with a horizontal side burrow a couple of centimetres down. Neohela monstrosa appears to feeds on newly settled detritus that it collects from the surface sediment through the use of its long antennae while the burrow is mainly used for protection against predators such as demersal fish. Newly released juveniles are probably kept in the burrow for protection. Based on the local high density of N. monstrosa together with its habit of making long burrows, we suggest that there is significant bioturbation associated with the presence of N. monstrosa in deep sedimentary habitats of the Norwegian Sea, which likely provides an important ecosystem function.     

Effect of vagal denervation on insulin release after oral and intravenous glucose

Zusammenfassung Perorale Glykosebelastung ergab bei vagotomierten Ratten Erhöhung des Blutglykosespiegels. Nach intravenöser Glykosezufuhr wurden niedrigere Werte von immunoreaktivem Insulin im Serum gefunden. Ebenso war der insulinogene Index bedeutend niedriger sowohl nach peroraler als auch nach intravenöser Glykosezufuhr. Vagotomie dürfte somit die glykosebedingte Insulinfreisetzung reduzieren.     

The ATM-Chk2-Cdc25A checkpoint pathway guards against radioresistant DNA synthesis

When exposed to ionizing radiation (IR), eukaryotic cells activate checkpoint pathways to delay the progression of the cell cycle. Defects in the IR-induced S-phase checkpoint cause 'radioresistant DNA synthesis', a phenomenon that has been identified in cancer-prone patients suffering from ataxia-telangiectasia, a disease caused by mutations in the ATM gene. The Cdc25A phosphatase activates the cyclin-dependent kinase 2 (Cdk2) needed for DNA synthesis, but becomes degraded in response to DNA damage or stalled replication. Here we report a functional link between ATM, the checkpoint signalling kinase Chk2/Cds1 (Chk2) and Cdc25A, and implicate this mechanism in controlling the S-phase checkpoint. We show that IR-induced destruction of Cdc25A requires both ATM and the Chk2-mediated phosphorylation of Cdc25A on serine 123. An IR-induced loss of Cdc25A protein prevents dephosphorylation of Cdk2 and leads to a transient blockade of DNA replication. We also show that tumour-associated Chk2 alleles cannot bind or phosphorylate Cdc25A, and that cells expressing these Chk2 alleles, elevated Cdc25A or a Cdk2 mutant unable to undergo inhibitory phosphorylation (Cdk2AF) fail to inhibit DNA synthesis when irradiated. These results support Chk2 as a candidate tumour suppressor, and identify the ATM-Chk2-Cdc25A-Cdk2 pathway as a genomic integrity checkpoint that prevents radioresistant DNA synthesis.     

Crossed reflex actions evoked by high threshold muscle afferents

Résumé Chez le chat spinal des impulsions provoquées dans les fibres afférentes à seuil élevé d'origine musculaire chez le chat spinal facilitent ou inhibent des motoneurones contra-latéraux fléchisseurs et extenseurs. Chez l'animal décérébré, ces actions croisées sont supprimées, tandis qu'après une lésion pontine, les actions inhibitrices se manifestent.     

Human and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA

Repair of DNA damage is essential for maintaining genome integrity, and repair deficiencies in mammals are associated with cancer, neurological disease and developmental defects. Alkylation damage in DNA is repaired by at least three different mechanisms, including damage reversal by oxidative demethylation of 1-methyladenine and 3-methylcytosine by Escherichia coli AlkB. By contrast, little is known about consequences and cellular handling of alkylation damage to RNA. Here we show that two human AlkB homologues, hABH2 and hABH3, also are oxidative DNA demethylases and that AlkB and hABH3, but not hABH2, also repair RNA. Whereas AlkB and hABH3 prefer single-stranded nucleic acids, hABH2 acts more efficiently on double-stranded DNA. In addition, AlkB and hABH3 expressed in E. coli reactivate methylated RNA bacteriophage MS2 in vivo, illustrating the biological relevance of this repair activity and establishing RNA repair as a potentially important defence mechanism in living cells. The different catalytic properties and the different subnuclear localization patterns shown by the human homologues indicate that hABH2 and hABH3 have distinct roles in the cellular response to alkylation damage.     

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.     

Subendothelial retention of atherogenic lipoproteins in early atherosclerosis

Complications of atherosclerosis are the most common cause of death in Western societies. Among the many risk factors identified by epidemiological studies, only elevated levels of lipoproteins containing apolipoprotein (apo) B can drive the development of atherosclerosis in humans and experimental animals even in the absence of other risk factors. However, the mechanisms that lead to atherosclerosis are still poorly understood. We tested the hypothesis that the subendothelial retention of atherogenic apoB-containing lipoproteins is the initiating event in atherogenesis. The extracellular matrix of the subendothelium, particularly proteoglycans, is thought to play a major role in the retention of atherogenic lipoproteins. The interaction between atherogenic lipoproteins and proteoglycans involves an ionic interaction between basic amino acids in apoB100 and negatively charged sulphate groups on the proteoglycans. Here we present direct experimental evidence that the atherogenicity of apoB-containing low-density lipoproteins (LDL) is linked to their affinity for artery wall proteoglycans. Mice expressing proteoglycan-binding-defective LDL developed significantly less atherosclerosis than mice expressing wild-type control LDL. We conclude that subendothelial retention of apoB100-containing lipoprotein is an early step in atherogenesis.