Articles in 2007

A new method, SYNERGY, has been developed to systematically map the detailed evolutionary history of gene duplication and loss. This strategy was applied to the genomes of 17 Ascomycota fungal species to provide a comprehensive overview of gene duplication and loss in the yeast lineage and the biological constraints that govern gene evolution.

Generation of the organizer tissue is induced on the dorsal side of the developing embryo by an asymmetry in Nodal signalling, which is only sufficiently high dorsally to induce organizer-specific gene expression. Now, through the identification of a microRNA (miR-15 and miR-16) that targets the Nodal receptor, microRNA is shown to have a role in this process.

Targeted deletion of SAPAP3, a postsynaptic scaffolding protein expressed in the striatum, yields a behavioral phenotype with many characteristics of obsessive compulsive disorder (OCD). SAPAP3^−/− mice compulsively overgroom themselves and are unusually anxious. Behavioral symptoms are alleviated by SSRIs, and both behaviour and physiological abnormalities are rescued by lentiviral-mediated expression of SAPAP3 in the striatum.

This paper reports the observation of a step-by-step state collapse by using atoms to non-destructively measure the photon number of a field stored in a cavity. The procedure illustrates all the postulates of quantum measurement and should facilitate studies of non-classical fields trapped in cavities.

This paper describes the first evidence of a role for gap junctions in neuronal migration, and also shows that the adhesive properties of the gap junctions, not the conductivity of their channels, are important for the migration.

The enzyme uracil DNA glycosylase does not actively extrude just the uracil base from the DNA helix to facilitate its removal; instead, transient, passive opening of thymine: adenine and uracil: adenine base pairs allows both thymine and uracil to become extrahelical, but only uracil can subsequently fit in the active site.

FAPP2 is a key component of the glycosphingolipid synthetic pathway, mediating non-vesicular transport of glucosylceramide from its site of synthesis at the cis-Golgi to the trans-Golgi for conversion into complex glycosphingolipids. FAPP2 therefore has an important role in determining the lipid composition of the plasma membrane, which is highly enriched in glycosphingolipids.

Female mice with genetic or physical lesions of the vomeronasal organ (VNO) display strikingly masculine sexual behavior, suggesting that the masculine circuitry is actually intact even in females but is normally suppressed by VNO function.

Changes in residual protein entropy are a potentially important component of the change in the free energy of protein association, but such thermodynamics have been virtually impossible to determine experimentally. Here the authors used solution NMR spectroscopy to show that the change in internal dynamics of calmodulin varies significantly on binding a variety of target domains, which indicates that changes in residual protein conformational entropy can contribute significantly to the free energy of protein-ligand association.

This paper reports the first crystal and electron microscopy structure of an individual septin and a heteromeric complex as well as linear septin filaments. The structure reveals that the G domain, which is conserved amongst all septins, serves as a universal building block for formation of a polymer. This domain interacts with other septins via conserved residues.

JASMONATE-INSENSITIVE 3 (JAI3) and a family of related proteins named JAZ (jasmonate-ZIM-domain) are identified. JAI3 and some of the other JAZ proteins interact with the SCF^COI1 ubiquitin ligase complex. Additionally JAI3 and JAZ1 interact with AtMyc2, a key transcriptional activator of jasmonate-regulated gene expression.

Members of the jasmonate ZIM-domain (JAZ) protein family are identified as key regulators of jasmonate signalling. Some of these function as repressors of jasmonate-responsive gene expression. The results suggest a model in which jasmonate ligands promote binding of the SCF^COI1 ubiquitin ligase complex to jasmonate repressors, resulting in their degradation.

A library of transgenic flies expressing RNAi in a conditional manner, for virtually every gene in the Drosophila melanogaster genome, has been generated. This resource will allow the community to test the function of every gene, in any cell type, at any development stage, or in response to various types of experimental stimulations.

Insulin-like growth factor II (IGF-II) has a direct role in the survival and self-renewal of pluripotent human embryonic stem cells (hESCs). Evidence is also provided that IGF-II is expressed by supportive hESC-derived fibroblasts that are produced by the hESC themselves, revealing that pluripotent hESCs produce their own supportive stem cell niche that is capable of supplying critical factors to maintain hESCs in culture.

A small inversion of chromosome 2p has been found in a significant proportion of non-small-cell lung cancer patients. This inversion gives rise to a fusion protein comprising portions of EML4 and the anaplastic lymphoma kinase, ALK, which functions as a transforming oncogenes. Oncogenic translocations are frequent in haematopoietic tumours, but have only rarely been found in solid tumours.

A recurrent mutation found in the akt1 gene has been identified in breast, ovarian and colorectal tumours. The crystal structure of the mutant protein is determined and it is found that the protein displays in increased plasma membrane localization and functions as an oncogene in vitro and in a mouse model for leukaemia.

Single-molecule-based sequencing technology is applied to generate genome-wide maps of chromatin modifications in mammalian cells. Histone marks can discriminate genes that are active, poised for activation, or stably repressed and therefore reflect cell state and developmental potential.

A computational approach is used to predict the function of an uncharacterized enzyme by docking high-energy intermediate forms of candidate metabolites into its purported binding site. The docking experiments predicted that the enzyme would be able to deaminate intermediates of 5-methylthioadenosine and S-adenosylhomocysteine, a prediction confirmed by biochemical experiments and examination of the X-ray crystal structure of the protein.

The distribution of long-lived radiogenic isotopes along the world's mid-ocean ridges can be used to map geochemical domains, reflecting contrasting refilling modes of the upper mantle. Refilling of the upper mantle in the Atlantic and Indian domains is slow and confined to localized upwellings, whereas in the Pacific, upwellings are comparatively much wider and more rapid.