Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity

We have utilized computational biology to screen GenBank for the presence of recently integrated Ya5 and Yb8 Alu family members. Our analysis identified 2640 Ya5 Alu family members and 1852 Yb8 Alu family members from the draft sequence of the human genome. We selected a set of 475 of these elements for detailed analyses. Analysis of the DNA sequences from the individual Alu elements revealed a low level of random mutations within both subfamilies consistent with the recent origin of these elements within the human genome. Polymerase chain reaction assays were used to determine the phylogenetic distribution and human genomic variation associated with each Alu repeat. Over 99 % of the Ya5 and Yb8 Alu family members were restricted to the human genome and absent from orthologous positions within the genomes of several non-human primates, confirming the recent origin of these Alu subfamilies in the human genome. Approximately 1 % of the analyzed Ya5 and Yb8 Alu family members had integrated into previously undefined repeated regions of the human genome. Analysis of mosaic Yb8 elements suggests gene conversion played an important role in generating sequence diversity among these elements. Of the 475 evaluated elements, a total of 106 of the Ya5 and Yb8 Alu family members were polymorphic for insertion presence/absence within the genomes of a diverse array of human populations. The newly identified Alu insertion polymorphisms will be useful tools for the study of human genomic diversity.     

Structural and biochemical alterations in Giardia lamblia cysts exposed to ozone

Because of its efficacy in inactivating waterborne protozoan cysts and oocysts, ozone is frequently used for disinfection of drinking water. The effect of ozone on cysts of Giardia lamblia was investigated in gerbils (Meriones unguiculatus), using an infectivity assay by scanning electron microscopy, immunoblotting, and flow cytometry. Cysts recovered from experimentally infected gerbils were exposed to an initial ozone concentration of 1.5 mg/L for 0, 30, 60, and 120 sec.This treatment resulted in a dose-dependent reduction in cysts concentration, loss of infectivity in gerbils, and profound structural modifications to the cyst wall. Exposure for 60 sec or longer resulted in extensive protein degradation and in the disappearance of a cyst wall and a trophozoite antigen.     

Patterns of ancestral human diversity: an analysis of Alu-insertion and restriction-site polymorphisms

We have analyzed 35 widely distributed, polymorphic Alu loci in 715 individuals from 31 world populations. The average frequency of Alu insertions (the derived state) is lowest in Africa (.42) but is higher and similar in India (.55), Europe (.56), and Asia (.57). A comparison with 30 restriction-site polymorphisms (RSPs) for which the ancestral state has been determined shows that the frequency of derived RSP alleles is also lower in Africa (.35) than it is in Asia (.45) and in Europe (.46). Neighbor-joining networks based on Alu insertions or RSPs are rooted in Africa and show African populations as separate from other populations, with high statistical support. Correlations between genetic distances based on Alu and nuclear RSPs, short tandem-repeat polymorphisms, and mtDNA, in the same individuals, are high and significant. For the 35 loci, Alu gene diversity and the diversity attributable to population subdivision is highest in Africa but is lower and similar in Europe and Asia. The distribution of ancestral alleles is consistent with an origin of early modern human populations in sub-Saharan Africa, the isolation and preservation of ancestral alleles within Africa, and an expansion out of Africa into Eurasia. This expansion is characterized by increasing frequencies of Alu inserts and by derived RSP alleles with reduced genetic diversity in non-African populations.     

Sea urchin Hox genes: insights into the ancestral Hox cluster

We describe the Hox cluster in the radially symmetric sea urchin and compare our findings to what is known from clusters in bilaterally symmetric animals. Several Hox genes from the direct-developing sea urchin Heliocidaris erythrogramma are described. CHEF gel analysis shows that the Hox genes are clustered on a < or = 300 kilobase (kb) fragment of DNA, and only a single cluster is present, as in lower chordates and other nonvertebrate metazoans. Phylogenetic analyses of sea urchin, amphioxus, Drosophila, and selected vertebrate Hox genes confirm that the H. erythrogramma genes, and others previously cloned from other sea urchins, belong to anterior, central, and posterior groups. Despite their radial body plan and lack of cephalization, echinoderms retain at least one of the anterior group Hox genes, an orthologue of Hox3. The structure of the echinoderm Hox cluster suggests that the ancestral deuterostome had a Hox cluster more similar to the current chordate cluster than was expected Sea urchins have at least three Abd-B type genes, suggesting that Abd-B expansion began before the radiation of deuterostomes.      

How important are aquatic predators to mosquito larval populations in natural wetlands? A case study from Carolina bays in Georgia

Predation is believed to be an important natural control on larval mosquito populations. However, empirical evidence for predator impacts is lacking, especially from natural wetlands (swamps and marshes). Over a 2-year period, we sampled larval mosquito populations and naturally co-occurring predator assemblages (aquatic invertebrates, fishes) from ten depressional wetlands (Carolina bays) located on a wildlife management area in east central Georgia. We collected a diversity of mosquito larvae and predators (odonates, bugs, beetles, flies, and fishes) from the wetlands, with predator numbers substantially exceeding mosquito larval numbers. However, using a community ecology approach with multivariate ordination and correlation techniques, we found no compelling evidence that these predators were controlling mosquito larval distributions (i.e. significant negative statistical associations were not detected). Those mosquitoes that successfully breed in Carolina bay wetlands (Culiseta melanura, Coquillettidia perturbans, Anopheles crucians) appear well adapted to co-exist with a plethora of naturally occurring predators.     

Clonal plant allocation to daughter ramets is a simple function of parent size across species and nutrient levels

The evolution of clonal growth is a widespread phenomenon among plant species, characterized by the production of genetically identical clonal fragments (ramets) via rhizomes or stolons that form an interconnected clonal organism (genet). Clonal plant species are known to differ in their investment into ramet production, and exhibit considerable variation in ramet morphology both within and among species. While patterns of resource allocation are thought to be linked to a number of plant characteristics, many analyses are limited by uncertainty in how clonal plants determine the morphology and resources allocated to new ramets. In this study, we attempted to discern what aspects of parent ramets best predicted resource allocation to new daughter ramets, and the relationship between resource allocation and daughter ramet rhizome morphology. We grew two sedge species, Schoenoplectus tabernaemontani and Eleocharis elliptica, in a greenhouse under two levels of fertilizer addition. By harvesting daughter ramets that had initiated stem production, yet remained aphotosynthetic, we were able to isolate parental investment into non-independent daughter ramets at a point where daughter ramet spacer length became fixed. Our results indicate that parent ramets allocated a non-linear proportion of parent rhizome biomass to the production of daughter ramets. Moreover, this relationship was unaffected by environmental nutrient availability. Daughter ramet biomass, in turn, was strongly correlated with daughter ramet spacer length. These observations shed light on key processes governing clonal growth in plants, and their potential application in unifying allocational and morphological perspectives to explore the fitness implications of variability in clonal growth.     

Amino acid size, charge, hydropathy indices and matrices for protein structure analysis

Background  

Prediction of protein folding and specific interactions from only the sequence (ab initio) is a major challenge in bioinformatics. It is believed that such prediction will prove possible if Anfinsen's thermodynamic principle is correct for all kinds of proteins, and all the information necessary to form a concrete 3D structure is indeed present in the sequence.