Design and analysis issues in genome-wide somatic mutation studies of cancer

The availability of the human genome sequence and progress in sequencing and bioinformatic technologies have enabled genome-wide investigation of somatic mutations in human cancers. This article briefly reviews challenges arising in the statistical analysis of mutational data of this kind. A first challenge is that of designing studies that efficiently allocate sequencing resources. We show that this can be addressed by two-stage designs and demonstrate via simulations that even relatively small studies can produce lists of candidate cancer genes that are highly informative for future research efforts. A second challenge is to distinguish mutated genes that are selected for by cancer (drivers) from mutated genes that have no role in the development of cancer and simply happened to mutate (passengers). We suggest that this question is best approached as a classification problem and discuss some of the difficulties of more traditional testing-based approaches. A third challenge is to identify biologic processes affected by the driver genes. This can be pursued by gene set analyses. These can reliably identify functional groups and pathways that are enriched for mutated genes even when the individual genes involved in those pathways or sets are not mutated at sufficient frequencies to provide conclusive evidence as drivers.     

Preparation of Na,K-ATPase specifically modified on the anti-fluorescein antibody-inaccessible site by fluorescein 5'-isothiocyanate

Specific labeling is required for energy transfer measurements and to avoid artifacts in the use of fluorophores as reporter groups. Therefore, a method for specific modification by one of the most popular reagents for P-type ATPases (fluorescein 5'-isothiocyanate) has been developed. Sulfhydryl reagents protected against modification of cysteine residues, and treatment with dithiothreitol eliminated a slow doubling of the fluorescence of conventionally modified Na,K-ATPase upon dilution that is attributed to disappearance of self-energy transfer. Removal of nonspecifically bound fluorescein was also confirmed by titration of the modified Na, K-ATPase with anti-fluorescein antibody and by time resolution of the fluorescence change when the modified enzyme was mixed with Na(+) in a stopped-flow instrument. The only fluorescence change when specifically modified Na,K-ATPase was mixed with Na(+) was the signal from fluorescein at the antibody-inaccessible, substrate-protectable site that reports the conformational change in unphosphorylated enzyme. The magnitude of the fluorescence change reporting the conformational change increased from between 8 and 12% to between 25 and 30% without affecting the kinetic constants estimated from titrations with Na(+) and K(+). The method should be generally applicable to the preparation of specifically labeled P-type pumps for use in kinetic and equilibrium titrations or energy transfer measurements.     

Graphene and graphene oxide: biofunctionalization and applications in biotechnology

Graphene is the basic building block of 0D fullerene, 1D carbon nanotubes, and 3D graphite. Graphene has a unique planar structure, as well as novel electronic properties, which have attracted great interests from scientists. This review selectively analyzes current advances in the field of graphene bioapplications. In particular, the biofunctionalization of graphene for biological applications, fluorescence-resonance-energy-transfer-based biosensor development by using graphene or graphene-based nanomaterials, and the investigation of graphene or graphene-based nanomaterials for living cell studies are summarized in more detail. Future perspectives and possible challenges in this rapidly developing area are also discussed.     

Seroprevalence of Toxoplasma gondii antibodies among Atayal aboriginal people and their hunting dogs in northeastern Taiwan

Atayal aborigines, living at an altitude of 1,500-1,600 m in northeastern Taiwan, still hunt for wild animals with the help of hunting dogs. In this study, the latex agglutination test (LAT) was used to detect sera anti-toxoplasma antibodies in this community as a measure of their exposure to Toxoplasma gondii. The positive rates for sera anti-toxoplasma antibodies were 21.8% and 19.6%, respectively, in 422 Atayal and 51 hunting dogs tested. Neither of the positive rates were found to be significantly different between male (22.1%) and female Atayal (21.4%), or between humans (21.8%) and dogs (19.6%) (P > 0.05) when compared by the Chi-Squared test (chi 2-test). A significant difference was observed between the positive rates in adults (28.3%) and children (18.7%) (P < 0.05), and the age pattern of prevalence is consistent with an increasing duration of exposure to Toxoplasma gondii with age. The consumption of raw liver of wild animals or insufficiently cooked meat may be the major mode of transmission of toxoplasmosis in Atayal.