BOOTSTRAP CONFIDENCE INTERVALS FROM ADAPTIVE SAMPLING OF AN INSECT POPULATION

We construct 90% normal, percentile, and bias-corrected and accelerated confidence intervals using a finite population bootstrapping algorithm based on adaptive sampling in an agroecosystem. We evaluate the interval estimates based on sampling simulations of a spatially arranged population of plots that contain counts of beet webworms and based on an adaptive condition that generates small networks. The sampling distributions of the original sample estimates and of the bootstrap estimates were generally similar and symmetric. The simulation coverages were from 84% to 90% and similar under any of the sample sizes and any of the three confidence interval types. This study also serves as an example of how adaptive sampling may be used to estimate population characteristics of insects in agroecosystems

Morphological Differences Among Eyeless Amphipods in the Genus Stygobromus Dwelling in Different Subterranean Habitats

The amphipod genus Stygobromus occurs in a variety of subterranean habitats in North America, including caves, phreatic (groundwater) lakes, and superficial subterranean habitats (seeps and epikarst). The habitats share the absence of light but differ in other features, such as pore size of the habitat, available food, and degree of seasonality. Measurements of body size, antennal size, and antennal segment number of type specimens were compared for 56 species occurring in the eastern United States. Except for differences in body size, differences among species in the four different habitats were not significant. Body size was related to relative pore size of the habitat, e.g., epikarst, with the smallest spaces, had the smallest species. However, in all habitats, there was one very large species (\u3e 15mm); these enigmatic species apparently occupy a distinct ecological niche, perhaps being more predatory. Differences in relative antennal size showed no significant differences among habitats, and differences in number of antennal segments were marginally significant (P = 0.06) among habitat types and not in the predicted pattern. Differences among habitats in seasonality and available food seemed to be a minor part of the selective environment; absence of light seemed to be a major part of the selective environment

Evolutionary History and Phylodynamics of Influenza A and B Neuraminidase (NA) Genes Inferred from Large- Scale Sequence Analyses

Background: Influenza neuraminidase (NA) is an important surface glycoprotein and plays a vital role in viral replication and drug development. The NA is found in influenza A and B viruses, with nine subtypes classified in influenza A. The complete knowledge of influenza NA evolutionary history and phylodynamics, although critical for the prevention and control of influenza epidemics and pandemics, remains lacking. Methodology/Principal findings: Evolutionary and phylogenetic analyses of influenza NA sequences using Maximum Likelihood and Bayesian MCMC methods demonstrated that the divergence of influenza viruses into types A and B occurred earlier than the divergence of influenza A NA subtypes. Twenty-three lineages were identified within influenza A, two lineages were classified within influenza B, and most lineages were specific to host, subtype or geographical location. Interestingly, evolutionary rates vary not only among lineages but also among branches within lineages. The estimated tMRCAs of influenza lineages suggest that the viruses of different lineages emerge several months or even years before their initial detection. The dN/dS ratios ranged from 0.062 to 0.313 for influenza A lineages, and 0.257 to 0.259 for influenza B lineages. Structural analyses revealed that all positively selected sites are at the surface of the NA protein, with a number of sites found to be important for host antibody and drug binding. Conclusions/Significance: The divergence into influenza type A and B from a putative ancestral NA was followed by the divergence of type A into nine NA subtypes, of which 23 lineages subsequently diverged. This study provides a better understanding of influenza NA lineages and their evolutionary dynamics, which may facilitate early detection of newly emerging influenza viruses and thus improve influenza surveillance

Characterization of the estrogen receptor transfected MCF10A breast cell line 139B6

There has been increasing evidence which suggests that abnormal expression of the estrogen receptor (ER) protein in nonmalignant breast tissue may be important in the carcinogenic process. To examine the effects of ER expression in immortalized nonmalignant mammary epithelial cells, an expression vector containing human ER cDNA was transfected into the ER negative human breast cells, MCF10A. Characterization of a clone stably expressing ER, 139B6, provided evidence for the regulated synthesis of a functional ER capable of binding estradiol-17β (E 2 ) and undergoing processing. Expression of the ER gene did not enable E 2 to stimulate endogenous genes [progesterone receptor (PgR), pS2, cathepsin D and TGFα] which normally respond to estrogens in breast cancer cells. The ER in 139B6 cells was, however, capable of inducing expression of an ERE-regulated reporter gene, indicating its ability to interact with transcriptional machinery. Furthermore, cultures in log growth displayed a slight increase in doubling time in the presence of E 2 . These results indicate that ER expression alone is not sufficient to induce a transformed phenotype. Thus, the 139B6 cell line should provide a new model for determining what additional changes lead to increased growth potential in response to E 2 and for exploring how E 2 itself may help bring about changes leading to progression of preneoplastic breast epithelial cells.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44202/1/10549_2005_Article_BF01806507.pd

PhyloMarker—A Tool for Mining Phylogenetic Markers Through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny

Molecular phylogeny is a fundamental tool to understanding the evolution of all life forms. One common issue faced by molecular phylogeny is the lack of sufficient molecular markers. Here, we present PhyloMarker, a phylogenomic tool designed to find nuclear gene markers for the inference of phylogeny through multiple genome comparison. Around 800 candidate markers were identified by PhyloMarker through comparison of partial genomes of Microcebus and Otolemur. In experimental tests of 20 randomly selected markers, nine markers were successfully amplified by PCR and directly sequenced in all 17 nominal Microcebus species. Phylogenetic analyses of the sequence data obtained for 17 taxa and nine markers confirmed the distinct lineage inferred from previous mtDNA data. PhyloMarker has also been used by other projects including the herons (Ardeidae, Aves) phylogeny and the Wood mice (Muridae, Mammalia) phylogeny. All source code and sample data are made available at http://bioinfo-srv1.awh.unomaha.edu/phylomarker/

Integrating complementary survey methods to estimate catches in Norway’s complex marine recreational hook-and-line fishery

Marine recreational fishing is popular in Norway, but current estimates of the catches by resident and tourist anglers are lacking due to several challenges, in particular Norway’s long and intricate coastline with no defined access points and the large tourist fishery. To test methods for long-term monitoring of boat-based marine recreational anglers, estimate their catches, and characterize the fishery, we conducted a roving creel survey based on a novel spatial sampling frame and a survey of tourist fishing businesses in Troms and Hordaland County. These surveys showed that cod (Gadus morhua) and saithe (Pollachius virens) dominated the catches in Troms, while mackerel (Scomber scombrus) and saithe dominated the catches in Hordaland. The estimated total annual harvest of cod by all marine recreational anglers was 2 160 tonnes (relative standard error, or RSE 44%) in Troms and 73 tonnes (RSE 29%) in Hordaland, of which ∼40% (in weight) were landed in registered tourist fishing businesses, based on data from the tourist fishing survey. The results indicate that recreational anglers in Hordaland harvest more cod in coastal waters than commercial fishers. This study provides information for developing marine recreational fisheries monitoring in challenging survey situations to support science-based fisheries management.publishedVersio

Genetic variation exists for telomeric array organization within and among the genomes of normal, immortalized, and transformed chicken systems

This study investigated telomeric array organization of diverse chicken genotypes utilizing in vivo and in vitro cells having phenotypes with different proliferation potencies. Our experimental objective was to characterize the extent and nature of array variation present to explore the hypothesis that mega-telomeres are a universal and fixed feature of chicken genotypes. Four different genotypes were studied including normal (UCD 001, USDA-ADOL Line 0), immortalized (DF-1), and transformed (DT40) cells. Both cytogenetic and molecular approaches were utilized to develop an integrated view of telomeric array organization. It was determined that significant variation exists within and among chicken genotypes for chromosome-specific telomeric array organization and total genomic-telomeric sequence content. Although there was variation for mega-telomere number and distribution, two mega-telomere loci were in common among chicken genetic lines (GGA 9 and GGA W). The DF-1 cell line was discovered to maintain a complex derivative karyotype involving chromosome fusions in the homozygous and heterozygous condition. Also, the DF-1 cell line was found to contain the greatest amount of telomeric sequence per genome (17%) as compared to UCD 001 (5%) and DT40 (1.2%). The chicken is an excellent model for studying unique and universal features of vertebrate telomere biology, and characterization of the telomere length variation among genotypes will be useful in the exploration of mechanisms controlling telomere length maintenance in different cell types having unique phenotypes

The relationship between cave biodiversity and available habitat

Aim:The goal of this study was to determine the role habitat availability plays in the distribution of obligate subterranean cave fauna in eastern North America. Location: The numbers of stygobites, troglobites and caves in the counties of the south‐eastern USA were analysed. Methods: The data were characterized by large numbers of zeroes and by spatial clustering of non‐zeroes in five regions. Regression and conditional autoregressive (CAR) models were used to elucidate the patterns and relationships between numbers of species and numbers of caves both locally and regionally. Results: Local effects (regions and numbers of caves in counties) accounted for 45% of the variation in troglobite counts (P =\u3c 0.001) and 24% of the variation in stygobite counts (P =\u3c 0.001). Significant spatial autocorrelation among both stygobites and troglobites (P =\u3c 0.0001) was found as well.Conclusion Overall, habitat availability as measured by cave numbers influenced species richness. Spatial and regional effects also played an important role in determining the observed distributions of the subterranean fauna. Terrestrial and aquatic communities showed very different patterns in their relationship to habitat and within the different regions