Insertional mutagenesis identifies multiple networks of cooperating genes driving intestinal tumorigenesis

The evolution of colorectal cancer suggests the involvement of many genes. To identify new drivers of intestinal cancer, we performed insertional mutagenesis using the Sleeping Beauty transposon system in mice carrying germline or somatic Apc mutations. By analyzing common insertion sites (CISs) isolated from 446 tumors, we identified many hundreds of candidate cancer drivers. Comparison to human data sets suggested that 234 CIS-targeted genes are also dysregulated in human colorectal cancers. In addition, we found 183 CIS-containing genes that are candidate Wnt targets and showed that 20 CISs-containing genes are newly discovered modifiers of canonical Wnt signaling. We also identified mutations associated with a subset of tumors containing an expanded number of Paneth cells, a hallmark of deregulated Wnt signaling, and genes associated with more severe dysplasia included those encoding members of the FGF signaling cascade. Some 70 genes had co-occurrence of CIS pairs, clustering into 38 sub-networks that may regulate tumor development.     

Regulating the large Sec7 ARF guanine nucleotide exchange factors: the when,where and how of activation

Eukaryotic cells require selective sorting and transport of cargo between intracellular compartments. This is accomplished at least in part by vesicles that bud from a donor compartment, sequestering a subset of resident protein “cargos” destined for transport to an acceptor compartment. A key step in vesicle formation and targeting is the recruitment of specific proteins that form a coat on the outside of the vesicle in a process requiring the activation of regulatory GTPases of the ARF family. Like all such GTPases, ARFs cycle between inactive, GDP-bound, and membrane-associated active, GTP-bound, conformations. And like most regulatory GTPases the activating step is slow and thought to be rate limiting in cells, requiring the use of ARF guanine nucleotide exchange factor (GEFs). ARF GEFs are characterized by the presence of a conserved, catalytic Sec7 domain, though they also contain motifs or additional domains that confer specificity to localization and regulation of activity. These domains have been used to define and classify five different sub-families of ARF GEFs. One of these, the BIG/GBF1 family, includes three proteins that are each key regulators of the secretory pathway. GEF activity initiates the coating of nascent vesicles via the localized generation of activated ARFs and thus these GEFs are the upstream regulators that define the site and timing of vesicle production. Paradoxically, while we have detailed molecular knowledge of how GEFs activate ARFs, we know very little about how GEFs are recruited and/or activated at the right time and place to initiate transport. This review summarizes the current knowledge of GEF regulation and explores the still uncertain mechanisms that position GEFs at “budding ready” membrane sites to generate highly localized activated ARFs.     

The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome

We determined the complete genome sequence of Clostridium difficile strain 630, a virulent and multidrug-resistant strain. Our analysis indicates that a large proportion (11%) of the genome consists of mobile genetic elements, mainly in the form of conjugative transposons. These mobile elements are putatively responsible for the acquisition by C. difficile of an extensive array of genes involved in antimicrobial resistance, virulence, host interaction and the production of surface structures. The metabolic capabilities encoded in the genome show multiple adaptations for survival and growth within the gut environment. The extreme genome variability was confirmed by whole-genome microarray analysis; it may reflect the organism's niche in the gut and should provide information on the evolution of virulence in this organism.     

Basigin is a receptor essential for erythrocyte invasion by Plasmodium falciparum

Erythrocyte invasion by Plasmodium falciparum is central to the pathogenesis of malaria. Invasion requires a series of extracellular recognition events between erythrocyte receptors and ligands on the merozoite, the invasive form of the parasite. None of the few known receptor-ligand interactions involved are required in all parasite strains, indicating that the parasite is able to access multiple redundant invasion pathways. Here, we show that we have identified a receptor-ligand pair that is essential for erythrocyte invasion in all tested P. falciparum strains. By systematically screening a library of erythrocyte proteins, we have found that the Ok blood group antigen, basigin, is a receptor for PfRh5, a parasite ligand that is essential for blood stage growth. Erythrocyte invasion was potently inhibited by soluble basigin or by basigin knockdown, and invasion could be completely blocked using low concentrations of anti-basigin antibodies; importantly, these effects were observed across all laboratory-adapted and field strains tested. Furthermore, Ok(a-) erythrocytes, which express a basigin variant that has a weaker binding affinity for PfRh5, had reduced invasion efficiencies. Our discovery of a cross-strain dependency on a single extracellular receptor-ligand pair for erythrocyte invasion by P. falciparum provides a focus for new anti-malarial therapies.     

Antibiotic resistance is ancient

The discovery of antibiotics more than 70 years ago initiated a period of drug innovation and implementation in human and animal health and agriculture. These discoveries were tempered in all cases by the emergence of resistant microbes. This history has been interpreted to mean that antibiotic resistance in pathogenic bacteria is a modern phenomenon; this view is reinforced by the fact that collections of microbes that predate the antibiotic era are highly susceptible to antibiotics. Here we report targeted metagenomic analyses of rigorously authenticated ancient DNA from 30,000-year-old Beringian permafrost sediments and the identification of a highly diverse collection of genes encoding resistance to β-lactam, tetracycline and glycopeptide antibiotics. Structure and function studies on the complete vancomycin resistance element VanA confirmed its similarity to modern variants. These results show conclusively that antibiotic resistance is a natural phenomenon that predates the modern selective pressure of clinical antibiotic use.     

Elastic arteries in a primitive vertebrate: Mechanics of the lamprey ventral aorta

Lampreys exhibit important structural and biochemical differences in their connective tissues relative to higher vertebrates. The lamprey ventral aorta wall, for example, is composed principally of microfibrils, not elastin and collagen as in higher vertebrates. Our working hypothesis was that this arrangement of microfibrils is primitive, but provides sufficient elastic behaviour to function as aortae in higher vertebrates. To support this hypothesis, we measured the mechanical properties of the ventral aorta wall of the lamprey, and showed that the architecture provides a mechanical structure that does produce functional mechanical properties similar to aortae in higher vertebrates.     

A photosynthetic alveolate closely related to apicomplexan parasites

Many parasitic Apicomplexa, such as Plasmodium falciparum, contain an unpigmented chloroplast remnant termed the apicoplast, which is a target for malaria treatment. However, no close relative of apicomplexans with a functional photosynthetic plastid has yet been described. Here we describe a newly cultured organism that has ultrastructural features typical for alveolates, is phylogenetically related to apicomplexans, and contains a photosynthetic plastid. The plastid is surrounded by four membranes, is pigmented by chlorophyll a, and uses the codon UGA to encode tryptophan in the psbA gene. This genetic feature has been found only in coccidian apicoplasts and various mitochondria. The UGA-Trp codon and phylogenies of plastid and nuclear ribosomal RNA genes indicate that the organism is the closest known photosynthetic relative to apicomplexan parasites and that its plastid shares an origin with the apicoplasts. The discovery of this organism provides a powerful model with which to study the evolution of parasitism in Apicomplexa.     

Leading Effective Global Virtual Teams: The Consequences of Methods of Communication

This paper explores the relationship between communication and team effectiveness within the context of global virtual teams, arguing that a range of communication methods may impact upon the team’s effectiveness. To explore this relationship empirically, we present a key informant insights based on the activities deployed by a participant in a global team. The paper reports on the team’s effectiveness, their communication strategies and the team’s psychological traits: trust, shared understanding and co-operation. Findings from the pattern matching analysis indicate that the limited range of communication methods available to a global virtual team was not a major contributing factor to a team’s effectiveness. The paper offers communication/management techniques that could be beneficial to the global virtual team leader in facilitating team effectiveness, highlighting some issues surrounding the level of dispersion within teams that could be further explored in future research.     

Occurrence of Ord's kangaroo rat ( Dipodomys ordii ) along its eastern distributional limit in Nebraska

Changes in land use continue to alter habitats throughout Nebraska, and few studies have examined how such changes affect distributional limits of mammals. The distribution of Ord’s kangaroo rat ( Dipodomys ordii ) was last examined in eastern Nebraska about 4 decades ago. We examined the current eastern distributional limits of D. ordii to see whether its range had expanded, contracted, or remained constant in the state since the 1960s. Based on our study, kangaroo rats have experienced little change in distribution during recent decades. Herein, we report on data for 8 counties without prior records and a marginal range extension, as well as comment on habitat, reproduction, and taxonomic status of kangaroo rats in eastern Nebraska. Los cambios en el uso del suelo siguen modificando los hábitats a lo largo del estado de Nebraska, y pocos estudios han examinado cómo estos cambios afectan los límites de distribución de los mamíferos. La última evaluación de la distribución de la rata canguro de Ord ( Dipodomys ordii ) en el este de Nebraska se llevó a cabo hace 4 décadas. Examinamos los límites orientales actuales de la distribución de D. ordii para ver si su área de distribución se ha expandido, contraído o permanecido igual en el estado desde los años 1960. Con base en nuestra investigación, es posible decir que la distribución de las ratas canguro ha cambiado poco en décadas recientes. Aquí reportamos datos para 8 condados para los cuales no existían registros anteriores e informamos sobre una pequeña expansión de su área de distribución. También comentamos sobre el hábitat, la reproducción y la situación taxonómica de las ratas canguro en el este de Nebraska.