bluuebunny/crossref_metadata_2025_split huggingface dataset:
eae36, a Locus on Mouse Chromosome 4, Controls Susceptibility to Experimental Allergic Encephalomyelitis in Older Mice and Mice Immunized in the Winter
Authors: Teuscher Cory , Doerge R W , Fillmore Parley D , Blankenhorn Elizabeth P 
Published: November 2005

AbstractGenetic factors are believed to contribute to multiple sclerosis (MS) susceptibility; however, strong evidence implicating intrinsic and environmental factors in the etiopathogenesis of MS also exists. Susceptibility to experimental allergic encephalomyelitis (EAE), the principal animal model of MS, is also influenced by nongenetic factors, including age and season at immunization. This suggests that age- and season-by-gene interactions exist and that different susceptibility loci may influence disease as a function of the two parameters. In this study, linkage analysis based on genome exclusion mapping was carried out using age and season at immunization restricted cohorts of (B10.S × SJL/J) F2 intercross mice in an effort to identify such linkages. Significant linkage of EAE to eae4 and eae5 was detected with 6- to 12-week-old and summer cohorts. In contrast, significant linkage of EAE to eae4 and eae5 was not detected with the &gt;12-week-old and winter/spring populations. Rather, significant linkage to D4Mit203 at 128.50 Mb on chromosome 4 was detected with animals that were &gt;12 weeks old at the time of immunization or were immunized in the winter. This previously unidentified locus has been designated eae36. These results support the existence of age- and season-by-gene-specific interactions in the genetic control of susceptibility to autoimmune inflammatory disease of the central nervous system and suggest that late-onset MS may be immunogenetically distinct.
Estimating the “Effective Number of Codons”: The Wright Way of Determining Codon Homozygosity Leads to Superior Estimates
Authors: Fuglsang Anders 
Published: November 2005

Abstract
In 1990, Frank Wright introduced a method for measuring synonymous codon usage bias in a gene by estimation of the “effective number of codons,” Nc. Several attempts have been made recently to improve Wright's estimate of Nc, but the methods that work in cases where a gene encodes a protein not containing all amino acids with degenerate codons have not been tested against each other. In this article I derive five new estimators of Nc and test them together with the two published estimators, using resampling under rigorous testing conditions. Estimation of codon homozygosity, F, turns out to be a key to the estimation of Nc. F can be estimated in two closely related ways, corresponding to sampling with or without replacement, the latter being what Wright used. The Nc methods that are based on sampling without replacement showed much better accuracy at short gene lengths than those based on sampling with replacement, indicating that Wright's homozygosity method is superior. Surprisingly, the methods based on sampling with replacement displayed a superior correlation with mRNA levels in Escherichia coli.
Assessing the Fidelity of Ancient DNA Sequences Amplified From Nuclear Genes
Authors: Binladen Jonas , Wiuf Carsten , Gilbert M Thomas P , Bunce Michael , Barnett Ross , Larson Greger , Greenwood Alex D , Haile James , Ho Simon Y W , Hansen Anders J , Willerslev Eske 
Published: November 2005

Abstract
To date, the field of ancient DNA has relied almost exclusively on mitochondrial DNA (mtDNA) sequences. However, a number of recent studies have reported the successful recovery of ancient nuclear DNA (nuDNA) sequences, thereby allowing the characterization of genetic loci directly involved in phenotypic traits of extinct taxa. It is well documented that postmortem damage in ancient mtDNA can lead to the generation of artifactual sequences. However, as yet no one has thoroughly investigated the damage spectrum in ancient nuDNA. By comparing clone sequences from 23 fossil specimens, recovered from environments ranging from permafrost to desert, we demonstrate the presence of miscoding lesion damage in both the mtDNA and nuDNA, resulting in insertion of erroneous bases during amplification. Interestingly, no significant differences in the frequency of miscoding lesion damage are recorded between mtDNA and nuDNA despite great differences in cellular copy numbers. For both mtDNA and nuDNA, we find significant positive correlations between total sequence heterogeneity and the rates of type 1 transitions (adenine → guanine and thymine → cytosine) and type 2 transitions (cytosine → thymine and guanine → adenine), respectively. Type 2 transitions are by far the most dominant and increase relative to those of type 1 with damage load. The results suggest that the deamination of cytosine (and 5-methyl cytosine) to uracil (and thymine) is the main cause of miscoding lesions in both ancient mtDNA and nuDNA sequences. We argue that the problems presented by postmortem damage, as well as problems with contamination from exogenous sources of conserved nuclear genes, allelic variation, and the reliance on single nucleotide polymorphisms, call for great caution in studies relying on ancient nuDNA sequences.
High Mobility Group Proteins HMGD and HMGZ Interact Genetically With the Brahma Chromatin Remodeling Complex in Drosophila
Authors: Ragab Anan , Thompson Elizabeth C , Travers Andrew A 
Published: November 2005

Abstract
Many pleiotropic roles have been ascribed to small abundant HMG–Box (HMGB) proteins in higher eukaryotes but their precise function has remained enigmatic. To investigate their function genetically we have generated a defined deficiency uncovering the functionally redundant genes encoding HMGD and HMGZ, the Drosophila counterparts of HMGB1–3 in mammals. The resulting mutant is a strong hypomorphic allele of HmgD/Z. Surprisingly this allele is viable and exhibits only minor morphological defects even when homozygous. However, this allele interacts strongly with mutants of the Brahma chromatin remodeling complex, while no interaction was observed with mutant alleles of other remodeling complexes. We also observe genetic interactions between the HmgD/Z deficiency and some, but not all, known Brahma targets. These include the homeotic genes Sex combs reduced and Antennapedia, as well as the gene encoding the cell-signaling protein Rhomboid. In contrast to more general structural roles previously suggested for these proteins, we infer that a major function of the abundant HMGB proteins in Drosophila is to participate in Brahma-dependent chromatin remodeling at a specific subset of Brahma-dependent promoters.
Differential Usage of Alternative Pathways of Double-Strand Break Repair in Drosophila
Authors: Preston Christine R , Flores Carlos C , Engels William R 
Published: November 2005

Abstract
Double-strand DNA breaks can be repaired by any of several alternative mechanisms that differ greatly in the nature of the final repaired products. We used a reporter construct, designated “Repair reporter 3” (Rr3), to measure the relative usage of these pathways in Drosophila germ cells. The method works by creating a double-strand break at a specific location such that expression of the red fluorescent protein, DsRed, in the next generation can be used to infer the frequency at which each pathway was used. A key feature of this approach is that most data come from phenotypic scoring, thus allowing large sample sizes and considerable precision in measurements. Specifically, we measured the proportion of breaks repaired by (1) conversion repair, (2) nonhomologous end joining (NHEJ), or (3) single-strand annealing (SSA). For conversion repair, the frequency of mitotic crossing over in the germ line indicates the relative prevalence of repair by double Holliday junction (DHJ) formation vs. the synthesis-dependent strand annealing (SDSA) pathway. We used this method to show that breaks occurring early in germ-line development were much more frequently repaired via single-strand annealing and much less likely to be repaired by end joining compared with identical breaks occurring later in development. Conversion repair was relatively rare when breaks were made either very early or very late in development, but was much more frequent in between. Significantly, the changes in relative usage occurred in a compensatory fashion, such that an increase in one pathway was accompanied by decreases in others. This negative correlation is interpreted to mean that the pathways for double-strand break repair compete with each other to handle a given breakage event.
The Maize aberrant pollen transmission 1 Gene Is a SABRE/KIP Homolog Required for Pollen Tube Growth
Authors: Xu Zhennan , Dooner Hugo K 
Published: November 2005

Abstract
Maize (Zea mays) pollen tubes grow in the styles at a rate of &gt;1 μm/sec. We describe here a gene required to attain that striking rate. The aberrant pollen transmission 1 (apt1) gene of maize was identified by an Ac-tagged mutation that displayed a severe pollen transmission deficit in heterozygotes. Rare apt1 homozygotes can be recovered, aided by phenotypic selection for Ac homozygotes. Half of the pollen in heterozygotes and most of the pollen in homozygotes germinate short and twisted pollen tubes. The apt1 gene is 26 kb long, makes an 8.6-kb pollen-specific transcript spliced from 22 exons, and encodes a protein of 2607 amino acids. The APT1 protein is homologous to SABRE and KIP, Arabidopsis proteins of unknown function involved in the elongation of root cortex cells and pollen tubes, respectively. Subcellular localization analysis demonstrates that APT1 colocalizes with a Golgi protein marker in growing tobacco pollen tubes. We hypothesize that the APT1 protein is involved in membrane trafficking and is required for the high secretory demands of tip growth in pollen tubes. The apt1-m1(Ac) mutable allele is an excellent tool for selecting Ac transpositions because of the strong negative selection pressure operating against the parental Ac site.
Transposon Insertions ofmagellan-4That Impair Social Gliding Motility inMyxococcus xanthus
Authors: Youderian Philip , Hartzell Patricia L 
Published: November 2005

AbstractMyxococcus xanthus has two different mechanisms of motility, adventurous (A) motility, which permits individual cells to glide over solid surfaces, and social (S) motility, which permits groups of cells to glide. To identify the genes involved in S-gliding motility, we mutagenized a ΔaglU (A−) strain with the defective transposon, magellan-4, and screened for S− mutants that form nonmotile colonies. Sequence analysis of the sites of the magellan-4 insertions in these mutants and the alignment of these sites with the M. xanthus genome sequence show that two-thirds of these insertions lie within 27 of the 37 nonessential genes known to be required for social motility, including those necessary for the biogenesis of type IV pili, exopolysaccharide, and lipopolysaccharide. The remaining insertions also identify 31 new, nonessential genes predicted to encode both structural and regulatory determinants of S motility. These include three tetratricopeptide repeat proteins, several regulators of transcription that may control the expression of genes involved in pilus extension and retraction, and additional enzymes involved in polysaccharide metabolism. Three insertions that abolish S motility lie within genes predicted to encode glycolytic enzymes, suggesting that the signal for pilus retraction may be a simple product of exopolysaccharide catabolism.
Relaxation of Selection With Equalization of Parental Contributions in Conservation Programs: An Experimental Test With Drosophila melanogaster
Authors: Rodríguez-Ramilo S T , Morán P , Caballero A 
Published: November 2005

Abstract
Equalization of parental contributions is one of the most simple and widely recognized methods to maintain genetic diversity in conservation programs, as it halves the rate of increase in inbreeding and genetic drift. It has, however, the negative side effect of implying a reduced intensity of natural selection so that deleterious genes are less efficiently removed from the population with possible negative consequences on the reproductive capacity of the individuals. Theoretical results suggest that the lower fitness resulting from equalization of family sizes relative to that for free contribution schemes is expected to be substantial only for relatively large population sizes and after many generations. We present a long-term experiment with Drosophila melanogaster, comparing the fitness performance of lines maintained with equalization of contributions (EC) and others maintained with no management (NM), allowing for free matings and contributions from parents. Two (five) replicates of size N = 100 (20) individuals of each type of line were maintained for 38 generations. As expected, EC lines retained higher gene diversity and allelic richness for four microsatellite markers and a higher heritability for sternopleural bristle number. Measures of life-history traits, such as egg-to-adult viability, mating success, and global fitness declined with generations, but no significant differences were observed between EC and NM lines. Our results, therefore, provide no evidence to suggest that equalization of family sizes entails a disadvantage on the reproductive capacity of conserved populations in comparison with no management procedures, even after long periods of captivity.
Pleiotropic Costs of Niche Expansion in the RNA Bacteriophage Φ6
Authors: Duffy Siobain , Turner Paul E , Burch Christina L 
Published: November 2005

Abstract
Natural and experimental systems have failed to universally demonstrate a trade-off between generalism and specialism. When a trade-off does occur it is difficult to attribute its cause to antagonistic pleiotropy without dissecting the genetic basis of adaptation, and few previous experiments provide these genetic data. Here we investigate the evolution of expanded host range (generalism) in the RNA virus Φ6, an experimental model system allowing adaptive mutations to be readily identified. We isolated 10 spontaneous host range mutants on each of three novel Pseudomonas hosts and determined whether these mutations imposed fitness costs on the standard laboratory host. Sequencing revealed that each mutant had one of nine nonsynonymous mutations in the Φ6 gene P3, important in host attachment. Seven of these nine mutations were costly on the original host, confirming the existence of antagonistic pleiotropy. In addition to this genetically imposed cost, we identified an epigenetic cost of generalism that occurs when phage transition between host types. Our results confirm the existence in Φ6 of two costs of generalism, genetic and environmental, but they also indicate that the cost is not always large. The possibility for cost-free niche expansion implies that varied ecological conditions may favor host shifts in RNA viruses.
Efficacy of Formalin as an Egg Disinfectant for Improving Hybrid Catfish (Channel Catfish × Blue Catfish) Hatching Success
Authors: Small Brian C , Chatakondi Nagaraj 
Published: November 2005

Abstract
Formalin is currently the only aquaculture drug approved by the U.S. Food and Drug Administration for the control of fungi on the eggs of all finfish. The efficacy of formalin for disinfecting hybrid catfish (channel catfish Ictalurus punctatus × blue catfish I. furcatus) eggs was examined and compared with that of three other potential chemotherapeutants. Two experiments were conducted to evaluate treatment dose and frequency on the hatching success of the hybrid catfish. In the first experiment, hybrid catfish egg masses were divided and assigned to 1 of 13 treatments administered as daily 15-min baths. The treatments were as follows: (1) control (no treatment), (2) 50 ppm (mg/L) formalin (F), (3) 100 ppm F, (4) 200 ppm F, (5) 125 ppm hydrogen peroxide (HP), (6) 250 ppm HP, (7) 500 ppm HP, (8) 50 ppm povidone iodine (PI), (9) 100 ppm PI, (10) 200 ppm PI, (11) 2.5 ppm copper sulfate (CS), (12) 5 ppm CS, and (13) 10 ppm CS. Hatching success tended to be highest among eggs treated with 100 ppm F (87.7%), 2.5 ppm CS (87.0%), or 100 ppm PI (85.2%), although these success rates were not significantly (P &gt; 0.05) different from that in the control treatment (82.8%). Treatment with 500 ppm HP resulted in a significant (P &lt; 0.05) decrease in hatching success (31.5%). In the second experiment, the optimal frequency of formalin treatments was assessed by treating hybrid catfish eggs zero, two, three, or four times daily. Eggs treated three times daily with 100 ppm F had the highest (P &lt; 0.05) percentage of hatched eggs. To maximize hatching success, three daily treatments of hybrid catfish eggs with 100 ppm F as a 15-min bath is recommended.
A Three-Year Survey of Penaeid Shrimp and Callinectid Crabs from Texas Coastal Waters for Signs of Disease Caused by White Spot Syndrome Virus or Taura Syndrome Virus
Authors: Dorf Barbara A. , Hons Charlene , Varner Patricia 
Published: November 2005

Abstract
The Gulf of Mexico has the largest shrimp industry in the United States, including both natural fisheries and aquaculture resources. Aquaculture production comes primarily from Texas shrimp farms. With intensification of the farmed shrimp industry and international commerce in aquatic species, the incidence of infectious disease outbreaks has become a growing problem. In 1995, the Texas farmed shrimp industry suffered heavy losses during an outbreak of Taura syndrome virus. Rapid disease transmission, in conjunction with high pond mortalities during the grow-out season, revealed the need for a structured preventive health plan with stringent biosecurity measures. In addition, native indigenous shrimp and crab species have never been systematically evaluated for infectious disease agents. Concern for these native species prompted the Texas Parks and Wildlife Department to initiate a survey to evaluate the general health status of select indigenous marine invertebrate species along the Texas coast. From October 1997 through September 2000, 5,399 commercially important wild penaeid shrimp (2,009 white shrimp Litopenaeus setiferus, 2,868 brown shrimp Farfantepenaeus aztecus, and 522 pink shrimp F. duorarum) and 935 crabs (630 blue crabs Callinectes sapidus and 305 lesser blue crabs C. similis) were collected from randomly selected locations in nine Texas coastal bay systems and evaluated for known viral pathogens with the use of histopathology and in situ hybridization. In this study, only the virus Baculovirus penaei was detected in three brown shrimp. Taura syndrome virus and white spot syndrome virus were not detected within the testing limitations of this study.
Identification and Prediction of Fish Assemblages in Streams of the Mid‐Atlantic Highlands, USA
Authors: Cyterski Michael , Barber Craig 
Published: November 2005

AbstractManagement of aquatic resources requires meaningful assessment endpoints on which to base decisions. In freshwater streams, assessment endpoints are often defined as fish communities. Given the limited resources available for environmental monitoring, having a means of predicting fish assemblages in streams where no sampling has yet occurred would be useful. Such a tool could be used for regional screening‐level analyses of fish communities and could be input into local‐scale model applications for evaluating management scenarios of stream degradation or restoration. In this study, a set of fish assemblages (a list of fish species and their corresponding relative abundances) representative of different stream types in the Mid‐Atlantic Highlands region of the United States was defined by use of a k‐means cluster analysis performed on relative abundance estimates. The cluster analysis produced 18 fish assemblages, and the following 14 species had the greatest relative abundance in at least one of the 18 assemblages: Eastern blacknose dace Rhinichthys atratulus, bluehead chub Nocomis leptocephalus, bluntnose minnow Pimephales notatus, brook trout Salvelinus fontinalis, central stoneroller Campostoma anomalum, creek chub Semotilus atromaculatus, fantail darter Etheostoma flabellare, mottled sculpin Cottus bairdii, mountain redbelly dace Phoxinus oreas, redbreast sunfish Lepomis auritus, rosyside dace Clinostomus funduloides, slimy sculpin Cottus cognatus, striped shiner Luxilus chrysocephalus, and white sucker Catostomus commersonii. A discriminant analysis was then used to predict a stream's potential fish assemblage based on stream and watershed characteristics. The discriminant function had a 42% success rate using the following predictors: Latitude, longitude, mean stream depth, percent urban area of the watershed, and percent fine gravel on the stream bottom. The discriminant function was validated with an independent data set from a regional data collection effort in West Virginia, resulting in 44% success when classifying observed stream fish communities.
Reliability of Linear Measurements on a Virtual Bilateral Cleft Lip and Palate Model
Authors: Oosterkamp Barbara C. M. , van der Meer Wicher J. , Rutenfrans Majelle , Dijkstra Pieter U. 
Published: November 2005

Objective: To assess the reliability and validity of measurements performed on three-dimensional virtual models of neonatal bilateral cleft lip and palate patients, compared with measurements performed on plaster cast models. Materials and Methods: Ten high-quality plaster cast models of bilateral cleft lip and palate patients were scanned with an LDI-scanner to obtain a three-dimensional virtual model. Linear measurements were performed on the plaster cast models using a digital caliper and also on the three-dimensional virtual model using Viscam RP version 2.1 software. The measurements were performed by two observers on two occasions. Results: Intraclass correlations ranging from .81 to .96 were found for all measurements except the measurement between the constructed reference point pr and reference point i (intraclass correlation = .40). A post hoc procedure in which top-view screen prints of the three-dimensional virtual model were used to perform the measurement between reference points pr and i demonstrated an intraclass coefficient of .90. Conclusions: Three-dimensional virtual models obtained by laser scanning neonatal cast models of bilateral cleft lip and palate patients can be used reliably and validly to perform linear measurements between existing reference points on the surface of the model using Viscam RP version 2.1 software. Measurements between reference points constructed outside the surface of the model cannot be validly performed on the three-dimensional virtual model with the software used in this study. For these measurements, top-view screen prints of the three-dimensional virtual model can be used.