Calculating the statistical significance of physical clusters of co-regulated genes in the genome: the role of chromatin in domain-wide gene regulation

Physical clusters of co-regulated, but apparently functionally unrelated, genes are present in many genomes. Despite the important implication that the genomic environment contributes appreciably to the regulation of gene expression, no simple statistical method has been described to identify physical clusters of co-regulated genes. Here we report the development of a model that allows the direct calculation of the significance of such clusters. We have implemented the derived statistical relation in a software program, Pyxis, and have analyzed a selection of Saccharomyces cerevisiae gene expression microarray data sets. We have identified many gene clusters where constituent genes exhibited a regulatory dependence on proteins previously implicated in chromatin structure. Specifically, we found that Tup1p-dependent gene domains were enriched close to telomeres, which suggested a new role for Tup1p in telomere silencing. In addition, we identified Sir2p-, Sir3p- and Sir4p-dependent clusters, which suggested the presence of Sir-mediated heterochromatin in previously unidentified regions of the yeast genome. We also showed the presence of Sir4p-dependent gene clusters bordering the HMRa heterothallic locus, which suggested leaky termination of the heterochromatin by the boundary elements. These results demonstrate the utility of Pyxis in identifying possible higher order genomic features that may contribute to gene regulation in extended domains.     

Identifying DNA-binding proteins using structural motifs and the electrostatic potential

Robust methods to detect DNA-binding proteins from structures of unknown function are important for structural biology. This paper describes a method for identifying such proteins that (i) have a solvent accessible structural motif necessary for DNA-binding and (ii) a positive electrostatic potential in the region of the binding region. We focus on three structural motifs: helix–turn-helix (HTH), helix–hairpin–helix (HhH) and helix–loop–helix (HLH). We find that the combination of these variables detect 78% of proteins with an HTH motif, which is a substantial improvement over previous work based purely on structural templates and is comparable to more complex methods of identifying DNA-binding proteins. Similar true positive fractions are achieved for the HhH and HLH motifs. We see evidence of wide evolutionary diversity for DNA-binding proteins with an HTH motif, and much smaller diversity for those with an HhH or HLH motif.     

Leucocytozoon (Apicomplexa: Leucocytozoidae) from West African birds, with descriptions of two species

Five species of Leucocytozoon were recovered from 35/828 birds of 95 species examined from 6 sites in West Africa between May 1995 and June 2001. Leucocytozoon pogoniuli n. sp. is described from the tinker barbets Pogoniulus subsulphureus and Pogoniulus atroflavus. Leucocytozoon trachyphoni n. sp. is described from the barbet Trachyphonus purpureus. No leucocytozoids have been reported previously in species of Pogoniulus. Leucocytozoon nectariniae was identified from the sunbird Nectarinia olivacea, and Leucocytozoon brimonti was recovered from 4 species of Pycnonotidae (bulbuls), all of which are new host records. We also report the first Leucocytozoon to be recovered from the phylogenetically isolated bird, Picathartes sp. (Picathartidae). This parasite is similar in appearance to Leucocytozoon sakharoffi, and probably represents a previously undescribed species. In view of the intraspecific variability and, frequently, relatively minor interspecific differences within Leucocytozoidae, we suggest that the development and application of molecular techniques would greatly advance understanding of speciation and relationships within this family.     

Importance of cellular microenvironment and circulatory dynamics in B cell immunotherapy

B cell immunotherapy has emerged as a mainstay in the treatment of lymphomas and autoimmune diseases. Although the microenvironment has recently been demonstrated to play critical roles in B cell homeostasis, its contribution to immunotherapy is unknown. To analyze the in vivo factors that regulate mechanisms involved in B cell immunotherapy, we used a murine model for human CD20 (hCD20) expression in which treatment of hCD20(+) mice with anti-hCD20 mAbs mimics B cell depletion observed in humans. We demonstrate in this study that factors derived from the microenvironment, including signals from the B cell-activating factor belonging to the TNF family/BLyS survival factor, integrin-regulated homeostasis, and circulatory dynamics of B cells define distinct in vivo mechanism(s) and sensitivities of cells in anti-hCD20 mAb-directed therapies. These findings provide new insights into the mechanisms of immunotherapy and define new opportunities in the treatment of cancers and autoimmune diseases.     

Invasion risks posed by the aquarium trade and live fish markets on the Laurentian Great Lakes

International trade is an important mechanism for global non-indigenous species introductions, which have had profound impacts on the biodiversity of aquatic ecosystems including the Laurentian Great Lakes. The best-documented vector by which non-indigenous species have entered the Great Lakes is ballast water discharged by transoceanic ships. A variety of potential alternative vectors exist, including the intentional release of aquarium or food organisms. To assess whether these vectors pose a significant invasion risk for the Great Lakes, we surveyed fish sold live in markets and fish, mollusks and macrophytes sold in pet and aquarium stores within the Great Lakes watershed. We evaluated invasion risk using information on species’ thermal tolerance, history of invasion elsewhere, and potential propagule loads as indicated by frequency of occurrence in shops. Our research suggests that both the aquarium industry and live fish markets represent potential sources of future invaders to the Great Lakes, including several aquarium fishes and macrophytes, as well as Asian carp species sold in fish markets. Currently, few regulatory mechanisms exist to control these potential vectors.     

Pteropsin: a vertebrate-like non-visual opsin expressed in the honey bee brain

Insects have excellent color vision based on the expression of different opsins in specific sets of photoreceptive cells. Opsins are members of the rhodopsin superfamily of G-protein coupled receptors, and are transmembrane proteins found coupled to light-sensitive chromophores in animal photoreceptors. Diversification of opsins during animal evolution provided the basis for the development of wavelength-specific behavior and color vision, but with the exception of the recently discovered non-visual melanopsins, vertebrate and invertebrate opsins have generally been viewed as representing distinct lineages. We report a novel lineage of insect opsins, designated pteropsins. On the basis of sequence analysis and intron location, pteropsins are more closely related to vertebrate visual opsins than to invertebrate opsins. Of note is that the pteropsins are missing entirely from the genome of drosophilid flies. In situ hybridization studies of the honey bee, Apis mellifera, revealed that pteropsin is expressed in the brain of this species and not in either the simple or compound eyes. It was also possible, on the basis of in situ hybridization studies, to assign different long wavelength opsins to the compound eyes (AmLop1) and ocelli (AmLop2). Insect pteropsin might be orthologous to a ciliary opsin recently described from the annelid Platynereis, and therefore represents the presence of this vertebrate-like light-detecting system in insects.     

Recurrent seascape units identify key ecological processes along the western Antarctic Peninsula

The western Antarctic Peninsula (WAP) is a bellwether of global climate change and natural laboratory for identifying interactions between climate and ecosystems. The Palmer Long‐Term Ecological Research (LTER) project has collected data on key ecological and environmental processes along the WAP since 1993. To better understand how key ecological parameters are changing across space and time, we developed a novel seascape classification approach based on in situ temperature, salinity, chlorophyll a, nitrate + nitrite, phosphate, and silicate. We anticipate that this approach will be broadly applicable to other geographical areas. Through the application of self‐organizing maps (SOMs), we identified eight recurrent seascape units (SUs) in these data. These SUs have strong fidelity to known regional water masses but with an additional layer of biogeochemical detail, allowing us to identify multiple distinct nutrient profiles in several water masses. To identify the temporal and spatial distribution of these SUs, we mapped them across the Palmer LTER sampling grid via objective mapping of the original parameters. Analysis of the abundance and distribution of SUs since 1993 suggests two year types characterized by the partitioning of chlorophyll a into SUs with different spatial characteristics. By developing generalized linear models for correlated, time‐lagged external drivers, we conclude that early spring sea ice conditions exert a strong influence on the distribution of chlorophyll a and nutrients along the WAP, but not necessarily the total chlorophyll a inventory. Because the distribution and density of phytoplankton biomass can have an impact on biomass transfer to the upper trophic levels, these results highlight anticipated links between the WAP marine ecosystem and climate.     

The International Mouse Phenotyping Consortium (IMPC): a functional catalogue of the mammalian genome that informs conservation

The International Mouse Phenotyping Consortium (IMPC) is building a catalogue of mammalian gene function by producing and phenotyping a knockout mouse line for every protein-coding gene. To date, the IMPC has generated and characterised 5186 mutant lines. One-third of the lines have been found to be non-viable and over 300 new mouse models of human disease have been identified thus far. While current bioinformatics efforts are focused on translating results to better understand human disease processes, IMPC data also aids understanding genetic function and processes in other species. Here we show, using gorilla genomic data, how genes essential to development in mice can be used to help assess the potentially deleterious impact of gene variants in other species. This type of analyses could be used to select optimal breeders in endangered species to maintain or increase fitness and avoid variants associated to impaired-health phenotypes or loss-of-function mutations in genes of critical importance. We also show, using selected examples from various mammal species, how IMPC data can aid in the identification of candidate genes for studying a condition of interest, deliver information about the mechanisms involved, or support predictions for the function of genes that may play a role in adaptation. With genotyping costs decreasing and the continued improvements of bioinformatics tools, the analyses we demonstrate can be routinely applied.