bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hypervariable Noncoding Sequences in Saccharomyces cerevisiaeSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY942206, AY942556.
Authors: Fay Justin C , Benavides Joseph A 
Published: June 2005

Abstract
Compared to protein-coding sequences, the evolution of noncoding sequences and the selective constraints placed on these sequences is not well characterized. To compare the evolution of coding and noncoding sequences, we have conducted a survey for DNA polymorphism at five randomly chosen loci among a diverse collection of 81 strains of Saccharomyces cerevisiae. Average rates of both polymorphism and divergence are 40% lower at noncoding sites and 90% lower at nonsynonymous sites in comparison to synonymous sites. Although noncoding and coding sequences show substantial variability in ratios of polymorphism to divergence, two of the loci, MLS1 and PDR10, show a higher rate of polymorphism at noncoding compared to synonymous sites. The high rate of polymorphism is not accompanied by a high rate of divergence and is limited to a few small regions. These hypervariable regions include sites with three segregating bases at a single site and adjacent polymorphic sites. We show that this clustering of polymorphic sites is significantly greater than one would expect on the basis of the spacing between polymorphic fourfold degenerate sites. Although hypervariable noncoding sequences could result from selection on regulatory mutations, they could also result from transient mutational hotspots.
Identification of Genetic Loci That Interact With cut During Drosophila Wing-Margin Development
Authors: Krupp Joshua J , Yaich Lauren E , Wessells Robert J , Bodmer Rolf 
Published: June 2005

Abstract
The Drosophila selector gene cut is a hierarchal regulator of external sensory organ identity and is required to pattern the sensory and nonsensory cells of the wing margin. Cut performs the latter function, in part, by maintaining expression of the secreted morphogen encoded by wingless (wg). We find that Cut is required for wing-margin sensory organ specification in addition to and independently of Wg maintenance. In addition, we performed a genetic modifier screen to identify other genes that interact with cut in the regulation of wing-margin patterning. In total, 45 genetic loci (35 gain-of-function and 10 loss-of-function loci) were identified by virtue of their ability to suppress the wing-margin defects resulting from gypsy retrotransposon-mediated insulation of the cut wing-margin enhancer. Further genetic characterization identified several subgroups of candidate cut interacting loci. One group consists of putative regulators of gypsy insulator activity. A second group is potentially required for the regulation of Cut expression and/or activity and includes longitudinals lacking, a gene that encodes a family of BTB-domain zinc-finger transcription factors. A third group, which includes a component of the Brahma chromatin remodeling complex encoded by moira, affects the level of Cut expression in two opposing ways by suppressing the gypsy-mediated ctK phenotype and enhancing the non-gypsy ct53d phenotype. This suggests that the Brahma complex modulates both enhancer-controlled transcription and gypsy-mediated gene insulation of the cut locus.
Molecular Evidence for Transcription of Genes on a B Chromosome in Crepis capillaris
Authors: Leach Carolyn R , Houben Andreas , Field Bruce , Pistrick Klaus , Demidov Dmitri , Timmis Jeremy N 
Published: June 2005

Abstract
Dispensable, supernumerary (B) chromosomes are found in diverse eukaryotic species. The origin and genetic consequences of B chromosomes have been the subjects of speculation for more than a century. Until now, there has been no molecular evidence that B chromosome DNA is transcribed and there is no unequivocal evidence as to their origin. B chromosomes are considered to be genetically inert although they appear to cause a variety of phenotypic effects. We report that members of one of two ribosomal RNA gene families that are confined to the B chromosomes of a plant, Crepis capillaris, are transcribed—thus providing the first molecular evidence of gene activity on B chromosomes. Sequence analysis of part of the A and B chromosome rRNA genes, together with comparisons with related species, indicates that the B chromosome rRNA genes originate from the A chromosome.
Contrasting Patterns of Polymorphism and Divergence on the Z Chromosome and Autosomes in Two Ficedula Flycatcher Species
Authors: Borge Thomas , Webster Matthew T , Andersson Gunilla , Saetre Glenn-Peter 
Published: June 2005

AbstractIn geographic areas where pied and collared flycatchers (Ficedula hypoleuca and F. albicollis) breed in sympatry, hybridization occurs, leading to gene flow (introgression) between the two recently diverged species. Notably, while such introgression is observable at autosomal loci it is apparently absent at the Z chromosome, suggesting an important role for genes on the Z chromosome in creating reproductive isolation during speciation. To further understand the role of Z-linked loci in the formation of new species, we studied genetic variation of the two species from regions where they live in allopatry. We analyzed patterns of polymorphism and divergence in introns from 9 Z-linked and 23 autosomal genes in pied and collared flycatcher males. Average variation on the Z chromosome is greatly reduced compared to neutral expectations based on autosomal diversity in both species. We also observe significant heterogeneity between patterns of polymorphism and divergence at Z-linked loci and a relative absence of polymorphisms that are shared by the two species on the Z chromosome compared to the autosomes. We suggest that these observations may indicate the action of recurrent selective sweeps on the Z chromosome during the evolution of the two species, which may be caused by sexual selection acting on Z-linked genes. Alternatively, reduced variation on the Z chromosome could result from substantially higher levels of introgression at autosomal than at Z-linked loci or from a complex demographic history, such as a population bottleneck.
Derivation and Growing Human Embryonic Stem Cells on Feeders Derived from Themselves
Authors: Wang Qian , Fang Zhen F. , Jin Fan , Lu Yong , Gai Hui , Sheng Hui Z. 
Published: June 2005

Abstract
Human embryonic stem cells (hESCs) are pluripotent. They have the potential to differentiate into every cell type of an organism. Since many human somatic cell types have the ability to support the growth of hESCs, cells differentiated from hESCs may also be able to support the growth of themselves. We tested this hypothesis by growing hESCs on feeders derived from themselves and demonstrated that such feeders did constitute an environment suitable for the derivation and long-term growth of hESCs. hESCs maintained in this system expressed all the markers indicative of the undifferentiated state and gave rise to cell types representative of all three primary germ layers upon differentiation. By modifying the genome of hESCs, feeders with special features can be derived and mass produced. The system will facilitate large-scale production of hESCs in a standardized animal pathogen-free environment.
Changes in productivity and contaminants in bald eagles nesting along the lower Columbia River, USA
Authors: Buck Jeremy A. , Anthony Robert G. , Schuler Carol A. , Isaacs Frank B. , Tillitt Donald E. 
Published: June 2005

Abstract
Previous studies documented poor productivity of bald eagles (Haliaeetus leucocephalus) in the lower Columbia River (LCR), USA, and elevated p,p′-dichlorodiphenyldichloroethylene (DDE), polychlorinated biphenyls (PCBs), dioxins, and furans in eagle eggs. From 1994 to 1995, we collected partially incubated eggs at 19 of 43 occupied territories along the LCR and compared productivity and egg contaminants to values obtained in the mid-1980s. We found higher productivity at new nesting sites along the river, yet productivity at 23 older breeding territories remained low and was not different (p = 0.713) between studies. Eggshell thickness at older territories had not improved (p = 0.404), and eggshells averaged 11% thinner than shells measured before dichlorodiphenyltrichloroethane use. Decreases in DDE (p = 0.022) and total PCBs (p = 0.0004) in eggs from older breeding areas occurred between study periods. Productivity was not correlated to contaminants, but DDE, PCBs, and dioxin-like chemicals exceeded estimated no-effect values. Some dioxin-like contaminants in eggs were correlated to nest location, with highest concentrations occurring toward the river's mouth where productivity was lowest. Although total productivity increased due to the success of new nesting pairs in the region, egg contaminants remain high enough to impair reproduction at older territories and, over time, may alter productivity of new pairs nesting near the river's mouth.
Mercury patterns in wood duck eggs from a contaminated reservoir in South Carolina, USA
Authors: Kennamer Robert A. , Stout Jason R. , Jackson Brian P. , Colwell Sheila V. , Brisbin I. Lehr , Burger Joanna 
Published: June 2005

Abstract
Mercury contamination of wildlife populations has been documented widely in recent years as biomonitoring has become an important tool for assessing environmental contamination. Avian eggs provide an ideal assay material for Hg biomonitoring, particularly when the collection of eggs is simplified by using cavity-nesting species that nest in easily monitored nest boxes. However, studies are needed that address the dynamics of how Hg is distributed within eggs, and how Hg is deposited naturally within clutches laid by a single female and among clutches laid by different females occupying the same contaminated environment. We collected 138 eggs from 13 complete clutches of box-nesting wood ducks (Aix sponsa) during 1991 and 1992 at a contaminated reservoir of the U.S. Department of Energy's Savannah River Site in South Carolina, USA. Total Hg residues in egg components and clutches were determined, partitioning of Hg among egg components was examined, and effects of egg-laying sequence on egg component Hg levels were determined. Mean albumen Hg was 0.22 ppm wet mass, mean yolk Hg was 0.04 ppm, and mean shell Hg was 0.03 ppm. On average, 86.1% of total egg Hg was concentrated in the albumen, 11.2% in the yolk, and 2.7% in the shell. Mercury concentrations in all egg components varied significantly among clutches and between successive clutches laid by the same female in the same year. Laying sequence significantly affected Hg concentrations in the albumen and shell, but not in the yolk. Declines of albumen Hg due to laying sequence were more pronounced for clutches that contained higher average Hg levels. Our results suggest that collection of first-laid eggs may be preferable for assessing maximal Hg exposure to developing embryos, and that monitoring Hg levels through the use of empty eggshells following brood departure from nests may be valid only if the laying sequence is known.
Effects of metal and organophosphate mixtures on Ceriodaphnia dubia survival and reproduction
Authors: Mahar Amy M. , Watzin Mary C. 
Published: June 2005

Abstract
The toxicity of mixtures of copper, zinc, and diazinon were determined for Ceriodaphnia dubia using 7-d survival and reproduction tests. Fifteen treatments, including combinations of the chemicals at 0, 25, 50, 75, and 100% of their individual median lethal concentrations, adding up to one toxic unit (TU) were tested. The TU was then used to classify each mixture response as additive, greater than additive, or less than additive. For survival, additive responses occurred in the 75% zinc plus 25% diazinon and the 50% copper plus 25% zinc plus 25% diazinon treatments. For reproduction, additive responses occurred in the 75% copper plus 25% zinc, 75% copper plus 25% diazinon, and 75% zinc plus 25% diazinon treatments. Copper and zinc played a greater role in toxicity than diazinon did. Less-than-additive interactions were found in all remaining mixtures, perhaps because of differences in mode of action between diazinon and metals. Consideration of dose-response curves can help to explain inconsistencies regarding toxic response in treatments with different ratios of the same chemicals. As TU percentages changed, mixture components were taken from different locations on differently shaped dose-response curves. Because most responses were less than additive, however, water-quality criteria based on individual concentrations probably are protective for most metal-organophosphate mixtures.
Interseasonal variation in blood concentrations of organochlorines in great black-backed gulls (Larus marinus)
Authors: Bustnes Jan Ove , Skaare Janneche Utne , Berg Vidar , Tveraa Torkild 
Published: June 2005

Abstract
In two subsequent breeding seasons (2001 and 2002), we measured 12 organochlorines (OCs), including hexa-chlorobenzene (HCB), β-hexachlorocyclohexane (β-HCH), p,p′-dichlorodiphenyldichloroethylene (DDE), oxychlordane, and eight polychlorinated biphenyl congeners (PCBs), in the blood of the same 25 great black-backed gulls (Larus marinus). The wet-weight concentrations of different OCs in the blood decreased between 45 and 60% from 2001 to 2002. The main reasons for this were lower blood-lipid concentrations and higher body condition in 2002 compared to 2001. The differences in blood lipids and body condition probably resulted from changes in the availability of different prey types between the years. Despite the variation in the blood concentrations of OCs, there was a high predictability of the relative relationship among individuals between the years, especially for the most-persistent compounds (persistent PCBs, oxychlordane, and DDE); that is, individuals with high levels in 2001 still had relatively high levels compared to other individuals in 2002. This suggests that a concentration obtained from a single blood sample is a relatively reliable measurement of OC burdens for individual great black-backed gulls compared to other individuals, independent of changes in mean OC levels within the population. However, by including information about the nutritional status of individuals, more precise interference from samples in different years and locations may be made. Moreover, the great seasonal variation in OC levels within individuals may have implications for how OC monitoring should be conducted in gull populations.
Cluster analysis of contaminated sediment data: Nodal analysis
Authors: Hartwell S. Ian , Claflin Larry W. 
Published: June 2005

Abstract
The objective of the present study was to explore the use of multivariate statistical methods as a means to discern relationships between contaminants and biological and/or toxicological effects in a representative data set from the National Status and Trends (NS&T) Program. Data from the National Oceanic and Atmospheric Administration, NS&T Program's Bioeffects Survey of Delaware Bay, USA, were examined using various univariate and multivariate statistical techniques, including cluster analysis. Each approach identified consistent patterns and relationships between the three types of triad data. The analyses also identified factors that bias the interpretation of the data, primarily the presence of rare and unique species and the dependence of species distributions on physical parameters. Sites and species were clustered with the unweighted pair-group method using arithmetic averages clustering with the Jaccard coefficient that clustered species and sites into mutually consistent groupings. Pearson product moment correlation coefficients, normalized for salinity, also were clustered. The most informative analysis, termed nodal analysis, was the intersection of species cluster analysis with site cluster analysis. This technique produced a visual representation of species association patterns among site clusters. Site characteristics, such as salinity and grain size, not contaminant concentrations, appeared to be the primary factors determining species distributions. This suggests the sediment-quality triad needs to use physical parameters as a distinct leg from chemical concentrations to improve sediment-quality assessments in large bodies of water. Because the Delaware Bay system has confounded gradients of contaminants and physical parameters, analyses were repeated with data from northern Chesapeake Bay, USA, with similar results.
Identification of six differentially expressed genes in response to copper exposure in the aquatic plant Lemna gibba (duckweed)
Authors: Akhtar Tariq A. , Lampi Mark A. , Greenberg Bruce M. 
Published: June 2005

Abstract
Aquatic plants are susceptible to metal pollution and provide an entry point for metals, such as copper, into the aquatic biosphere. Exposure of the aquatic plant Lemna gibba to copper has been associated with the production of reactive oxygen species (ROS) and oxidative damage, caused in large part by the ability of this metal to redox cycle. In particular, copper-mediated production of ROS, a known group of signaling molecules, triggers numerous defense responses in L. gibba. Therefore, the objective of the present study was to examine to what extent acute copper exposure alters gene expression. First, the kinetics of copper uptake was assessed to determine if assimilation occurred within the short exposures needed to induce gene expression. Subsequently, using differential display polymerase chain reaction, we identified six genes with expressions that were putatively altered in response to copper. Differential expression was confirmed by northern hybridization analysis and showed that copper causes an accumulation of transcripts that encode for callose synthase, heat shock protein 90, serine decarboxylase, and the biotin carboxylase subunit of acetyl-coenzyme A carboxylase. Conversely, copper caused a decline in transcript levels for genes encoding the HAP5 subunit of the heme-activated protein (HAP) transcription factor in addition to the chloroplast nucleoid DNA-binding protein CND41. Interestingly, the expressions of these genes are sensitive to cellular ROS levels. We believe that these gene products provide valuable information regarding the molecular mechanisms of copper toxicity.
Effects of dose and particle size on activated carbon treatment to sequester polychlorinated biphenyls and polycyclic aromatic hydrocarbons in marine sediments
Authors: Zimmerman John R. , Werner David , Ghosh Upal , Millward Rod N. , Bridges Todd S. , Luthy Richard G. 
Published: June 2005

Abstract
Recent laboratory studies show that mixing activated carbon with contaminated sediment reduces the chemical and biological availability of hydrophobic organic contaminants. In this study, we test the effects of varying the activated carbon dose and particle size in reducing the aqueous availability of polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs) and the uptake of PCBs by two benthic organisms. We mixed PCB- and PAH-contaminated sediment from Hunters Point Naval Shipyard, San Francisco Bay (CA, USA), for one month with activated carbon, at doses of 0.34, 1.7, and 3.4% dry mass basis. We found that increasing the carbon dose increased the effectiveness in reducing PCB bioaccumulation. In 56-d uptake tests with the benthic organisms Neanthes arenaceodentata and Leptocheirus plumulosus, PCB bioaccumulation was reduced by 93 and 90%, respectively, with 3.4% carbon. Increasing the dose also increased the effectiveness in reducing PCB and PAH aqueous concentrations and uptake by semipermeable membrane devices and quiescent flux of PCBs to overlying water. Decreasing activated carbon particle size increased treatment effectiveness in reducing PCB aqueous concentration, and larger-sized activated carbon (400–1,700 μm) was ineffective with a contact period of one month. We invoke a numerical model based on intraparticle diffusion in sediment and activated carbon particles to help interpret our experimental results. This model was useful in explaining the trends for the effect of activated carbon dose and particle size on PCB aqueous concentrations in well-mixed systems.
Monitoring exposure of northern cardinals, Cardinalis cardinalis, to cholinesterase-inhibiting pesticides: enzyme activity, reactivations, and indicators of environmental stress
Authors: Maul Jonathan D. , Farris Jerry L. 
Published: June 2005

Abstract
Northern cardinals (Cardinalis cardinalis) frequently use agricultural field edges in northeast Arkansas, USA, and may be at risk of exposure to cholinesterase (ChE)-inhibiting pesticides. We monitored northern cardinal exposure to ChE-inhibiting pesticides by comparing plasma total ChE (TChE) activity to reference-derived benchmarks and TChE reactivations. Total ChE and acetylcholinesterase (AChE) were measured for 128 plasma samples from 104 northern cardinals from nine study sites. Of birds sampled from sites treated with ChE-inhibiting pesticides, 4.3% of the samples had TChE activities below the diagnostic threshold (2 standard deviations [SD] below the reference mean) and 8.7% of the samples had TChE reactivations. No difference was found in TChE (p = 0.553) and AChE (p = 0.288) activity between treated and reference sites; however, activity varied among treated sites (p = 0.003). These data do not suggest uniform exposure to individuals, but rather exposure was variable and likely influenced by mitigating factors at individual and site scales. Furthermore, monitoring of TChE reactivation appeared to be a more sensitive indicator of exposure than the diagnostic threshold. Fluctuating asymmetry (FA) was greater at agricultural sites than reference sites (p = 0.016), supporting the hypothesis that FA may be useful for assessing a combination of habitat- and contaminant-related environmental stress.
Time trends (1983–1999) for organochlorines and polybrominated diphenyl ethers in rainbow smelt (Osmerus mordax) from lakes michigan, huron, and superior, USA
Authors: Chernyak Sergei M. , Rice Clifford P. , Quintal Richard T. , Begnoche Linda J. , Hickey James P. , Vinyard Bryan T. 
Published: June 2005

Abstract
The U.S. Geological Service Great Lakes Science Center has archived rainbow smelt (Osmerus mordax) collected from the early 1980s to the present. These fish were collected to provide time- and site-dependent contaminant residue data needed by researchers and managers to fill critical data gaps regarding trends and behavior of persistent organic contaminants in the Great Lakes ecosystem. In the present study, data are presented for concentrations of several organochlorine (OC) contaminants in the archived smelt, including DDT, polychlorinated biphenyls (PCBs), toxaphene, and chlordanes in Lakes Michigan and Huron (MI, USA) and in Lake Superior (MN, USA). The trends for all the OCs were declining as a first-order decay over the sampled time series (1983/1985–1993/1999) with the exception of toxaphene in Lake Superior and PCBs at the Charlevoix/Little Traverse Bay site in Lake Michigan. Concentration of the emerging contaminant, polybrominated diphenyl ethers (PBDEs), also was traced from its apparent entry into this ecosystem in approximately 1980 until 1999. Time trends for the PBDEs were increasing exponentially at all sites, with concentration-doubling times varying from 1.58 to 2.94 years.