A Taxonomic Search Engine: Federating taxonomic databases using web services

Background  

The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism.     

Comparative tests of ectoparasite species richness in seabirds

Background  

The diversity of parasites attacking a host varies substantially among different host species. Understanding the factors that explain these patterns of parasite diversity is critical to identifying the ecological principles underlying biodiversity. Seabirds (Charadriiformes, Pelecaniformes and Procellariiformes) and their ectoparasitic lice (Insecta: Phthiraptera) are ideal model groups in which to study correlates of parasite species richness. We evaluated the relative importance of morphological (body size, body weight, wingspan, bill length), life-history (longevity, clutch size), ecological (population size, geographical range) and behavioural (diving versus non-diving) variables as predictors of louse diversity on 413 seabird hosts species. Diversity was measured at the level of louse suborder, genus, and species, and uneven sampling of hosts was controlled for using literature citations as a proxy for sampling effort.     

Quality determination and the repair of poor quality spots in array experiments

Background  

A common feature of microarray experiments is the occurence of missing gene expression data. These missing values occur for a variety of reasons, in particular, because of the filtering of poor quality spots and the removal of undefined values when a logarithmic transformation is applied to negative background-corrected intensities. The efficiency and power of an analysis performed can be substantially reduced by having an incomplete matrix of gene intensities. Additionally, most statistical methods require a complete intensity matrix. Furthermore, biases may be introduced into analyses through missing information on some genes. Thus methods for appropriately replacing (imputing) missing data and/or weighting poor quality spots are required.     

The shape of human gene family phylogenies

Background  

The shape of phylogenetic trees has been used to make inferences about the evolutionary process by comparing the shapes of actual phylogenies with those expected under simple models of the speciation process. Previous studies have focused on speciation events, but gene duplication is another lineage splitting event, analogous to speciation, and gene loss or deletion is analogous to extinction. Measures of the shape of gene family phylogenies can thus be used to investigate the processes of gene duplication and loss. We make the first systematic attempt to use tree shape to study gene duplication using human gene phylogenies.     

Variations among cell lines in the synthesis of sphingolipids in de novo and recycling pathways

There are several pathways for the incorporation of sugars intoglycosphingolipids (GSL). Sugars can be added to ceramide that containssphinganine (dihydrosphingosine) synthesized de novo (pathway 1), toceramide synthesized from sphingoid bases produced by hydrolysis ofsphingolipids (pathway 2), and into GSL recycling from the endosomalpathway through the Golgi (pathway 3). We reported previously thesurprising observation that SW13 cells, a human adrenal carcinoma cellline, synthesize most of their GSL in pathway 2. We now present data on thesynthesis of GSL in four additional cell lines. Approximately 90% of sugarincorporation took place in pathway 2, and 10% or less in pathway 1, inhuman foreskin fibroblasts and NB41A3 neuroblastoma cells. In contrast,approximately 50-90% of sugar incorporation took place in pathway 1 inC2C12 myoblasts. The C2C12 cells divide more rapidly and synthesize 10-14times as much GSL as the other three cell lines. In C6 glioma cells,approximately 30% of sugar incorporation occurred in pathway 1 and 60% inpathway 2. There was no relation between the utilization of pathways forGSL and sphingomyelin synthesis in foreskin fibroblasts and C2C12 cells. Inboth cells pathways 1 and 2 each accounted for 50% of incorporation ofcholine into sphingomyelin. In five of the six cell lines that we havestudied, most GSL synthesis takes place in pathway 2. We suggest that whenthe need for synthesis is relatively low, as in slowly dividing cells, GSLare synthesized predominantly from sphingoid bases salvaged from thehydrolytic pathway. When cells are dividing more rapidly, the need forincreased synthesis is met by upregulating the de novo pathway.     

Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis

Using sequence data from the 28S ribosomal RNA (rRNA) genes of selected vertebrates, we investigated the effects that constraints imposed by secondary structure have on the phylogenetic analysis of rRNA sequence data. Our analysis indicates that characters from both base-pairing regions (stems) and non-base-pairing regions (loops) contain phylogenetic information, as judged by the level of support of the phylogenetic results compared with a well-established tree based on both morphological and molecular data. The best results (the greatest level of support of well-accepted nodes) were obtained when the complete data set was used. However, some previously supported nodes were resolved using either the stem or loop bases alone. Stem bases sustain a greater number of compensatory mutations than would be expected at random, but the number is < 40% of that expected under a hypothesis of perfect compensation to maintain secondary structure. Therefore, we suggest that in phylogenetic analyses, the weighting of stem characters be reduced by no more than 20%, relative to that of loop characters. In contrast to previous suggestions, we do not recommend weighting of stem positions by one-half, compared with that of loop positions, because this overcompensates for the constraints that selection imposes on the secondary structure of rRNA.