bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recently Evolved Genes Identified From Drosophila yakuba and D. erecta Accessory Gland Expressed Sequence Tags
Authors: Begun David J , Lindfors Heather A , Thompson Melissa E , Holloway Alisha K 
Published: December 2005

Abstract
The fraction of the genome associated with male reproduction in Drosophila may be unusually dynamic. For example, male reproduction-related genes show higher-than-average rates of protein divergence and gene expression evolution compared to most Drosophila genes. Drosophila male reproduction may also be enriched for novel genetic functions. Our earlier work, based on accessory gland protein genes (Acp's) in D. simulans and D. melanogaster, suggested that the melanogaster subgroup Acp's may be lost and/or gained on a relatively rapid timescale. Here we investigate this possibility more thoroughly through description of the accessory gland transcriptome in two melanogaster subgroup species, D. yakuba and D. erecta. A genomic analysis of previously unknown genes isolated from cDNA libraries of these species revealed several cases of genes present in one or both species, yet absent from ingroup and outgroup species. We found no evidence that these novel genes are attributable primarily to duplication and divergence, which suggests the possibility that Acp's or other genes coding for small proteins may originate from ancestrally noncoding DNA.
Chromosome Segment Duplications in Neurospora crassa and Their Effects on Repeat-Induced Point Mutation and Meiotic Silencing by Unpaired DNA
Authors: Vyas Meenal , Ravindran C , Kasbekar Durgadas P 
Published: December 2005

Abstract
The size and extent of four Neurospora crassa duplications, Dp(AR17), Dp(IBj5), Dp(OY329), and Dp(B362i), was determined by testing the coverage of RFLP markers. The first three duplications were all &gt;∼350 kb and have been shown in earlier studies to act as dominant suppressors of repeat-induced point mutation (RIP) in gene-sized duplications, possibly via titration of the RIP machinery. Dp(B362i), which is only ∼117 kb long, failed to suppress RIP. RIP suppression in gene-sized duplications by large duplications was demonstrated using another test gene, dow, and supposedly applies generally. Crosses homozygous for Dp(AR17) or Dp(IBj5) were as barren as heterozygous crosses. Barrenness of the heterozygous but not the homozygous crosses was suppressible by Sad-1, a semidominant suppressor of RNAi-dependent meiotic silencing by unpaired DNA. A model is proposed in which large duplications recessively suppress semidominant Sad-1 mutations. The wild-isolated Sugartown strain is hypothesized to contain a duplication that confers not only dominant suppression of RIP but also a barren phenotype, which is linked (9%) to supercontig 7.118 in LG VII.
New Arabidopsis Recombinant Inbred Line Populations Genotyped Using SNPWave and Their Use for Mapping Flowering-Time Quantitative Trait Loci
Authors: El-Lithy Mohamed E , Bentsink Leónie , Hanhart Corrie J , Ruys Gerda J , Rovito Daniela , Broekhof José L M , van der Poel Hein J A , van Eijk Michiel J T , Vreugdenhil Dick , Koornneef Maarten 
Published: December 2005

AbstractThe SNPWave marker system, based on SNPs between the reference accessions Colombia-0 and Landsberg erecta (Ler), was used to distinguish a set of 92 Arabidopsis accessions from various parts of the world. In addition, we used these markers to genotype three new recombinant inbred line populations for Arabidopsis, having Ler as a common parent that was crossed with the accessions Antwerp-1, Kashmir-2, and Kondara. The benefit of using multiple populations that contain many similar markers and the fact that all markers are linked to the physical map of Arabidopsis facilitates the quantitative comparison of maps. Flowering-time variation was analyzed in the three recombinant inbred line populations. Per population, four to eight quantitative trait loci (QTL) were detected. The comparison of the QTL positions related to the physical map allowed the estimate of 12 different QTL segregating for flowering time for which Ler has an allele different from one, two, or three of the other accessions.
Gene Action of New Mutations in Arabidopsis thaliana
Authors: Shaw Ruth G , Chang Shu-Mei 
Published: December 2005

Abstract
For a newly arising mutation affecting a trait under selection, its degree of dominance relative to the preexisting allele(s) strongly influences its evolutionary impact. We have estimated dominance parameters for spontaneous mutations in a subset of lines derived from a highly inbred founder of Arabidopsis thaliana by at least 17 generations of mutation accumulation (MA). The labor-intensive nature of the crosses and the anticipated subtlety of effects limited the number of MA lines included in this study to 8. Each MA line was selfed and reciprocally crossed to plants representing the founder genotype, and progeny were assayed in the greenhouse. Significant mutational effects on reproductive fitness included a recessive fitness-enhancing effect in one line and fitness-reducing effects, one additive and the other slightly recessive. Mutations conferring earlier phenology or smaller leaves were significantly recessive. For effects increasing leaf number and reducing height at flowering, additive gene action accounted for the expression of the traits. The sole example of a significantly dominant mutational effect delayed phenology. Our findings of recessive action of a fitness-enhancing mutational effect and additive action of a deleterious effect counter a common expectation of (partial) dominance of alleles that increase fitness, but the frequency of occurrence of such mutations is unknown.
Pleiotropic Quantitative Trait Loci Contribute to Population Divergence in Traits Associated With Life-History Variation in Mimulus guttatus
Authors: Hall Megan C , Basten Christopher J , Willis John H 
Published: December 2005

Abstract
Evolutionary biologists seek to understand the genetic basis for multivariate phenotypic divergence. We constructed an F2 mapping population (N = 539) between two distinct populations of Mimulus guttatus. We measured 20 floral, vegetative, and life-history characters on parents and F1 and F2 hybrids in a common garden experiment. We employed multitrait composite interval mapping to determine the number, effect, and degree of pleiotropy in quantitative trait loci (QTL) affecting divergence in floral, vegetative, and life-history characters. We detected 16 QTL affecting floral traits; 7 affecting vegetative traits; and 5 affecting selected floral, vegetative, and life-history traits. Floral and vegetative traits are clearly polygenic. We detected a few major QTL, with all remaining QTL of small effect. Most detected QTL are pleiotropic, implying that the evolutionary shift between these annual and perennial populations is constrained. We also compared the genetic architecture controlling floral trait divergence both within (our intraspecific study) and between species, on the basis of a previously published analysis of M. guttatus and M. nasutus. Eleven of our 16 floral QTL map to approximately the same location in the interspecific map based on shared, collinear markers, implying that there may be a shared genetic basis for floral divergence within and among species of Mimulus.
Chromosome-Level Homeology in Paleopolyploid Soybean (Glycine max) Revealed Through Integration of Genetic and Chromosome Maps
Authors: Walling Jason G , Shoemaker Randy , Young Nevin , Mudge Joann , Jackson Scott 
Published: December 2005

Abstract
Soybean has 20 chromosome pairs that are derived from at least two rounds of genomewide duplication or polyploidy events although, cytogenetically, soybean behaves like a diploid and has disomic inheritance for most loci. Genetically anchored genomic clones were used as probes for fluorescence in situ hybridization (FISH) to determine the level of postpolyploid chromosomal rearrangements and to integrate the genetic and physical maps to (1) assign linkage groups to specific chromosomes, (2) assess chromosomal structure, and (3) determine the distribution of recombination along the length of a chromosome. FISH mapping of seven putatively gene-rich BACs from linkage group L (chromosome 19) revealed that most of the genetic map correlates to the highly euchromatic long arm and that there is extensive homeology with another chromosome pair, although colinearity of some loci does appear to be disrupted. Moreover, mapping of BACs containing high-copy sequences revealed sequestration of high-copy repeats to the pericentromeric regions of this chromosome. Taken together, these data present a model of chromosome structure in a highly duplicated but diploidized eukaryote, soybean.
Fold Recognition of the Human Immunodeficiency Virus Type 1 V3 Loop and Flexibility of Its Crown Structure During the Course of Adaptation to a Host
Authors: Watabe Teruaki , Kishino Hirohisa , Okuhara Yoshiyasu , Kitazoe Yasuhiro 
Published: December 2005

Abstract
The third hypervariable (V3) region of the HIV-1 gp120 protein is responsible for many aspects of viral infectivity. The tertiary structure of the V3 loop seems to influence the coreceptor usage of the virus, which is an important determinant of HIV pathogenesis. Hence, the information about preferred conformations of the V3-loop region and its flexibility could be a crucial tool for understanding the mechanisms of progression from an initial infection to AIDS. Taking into account the uncertainty of the loop structure, we predicted the structural flexibility, diversity, and sequence fitness to the V3-loop structure for each of the sequences serially sampled during an asymptomatic period. Structural diversity correlated with sequence diversity. The predicted crown structure usage implied that structural flexibility depended on the patient and that the antigenic character of the virus might be almost uniform in a patient whose immune system is strong. Furthermore, the predicted structural ensemble suggested that toward the end of the asymptomatic period there was a change in the V3-loop structure or in the environment surrounding the V3 loop, possibly because of its proximity to the gp120 core.
Glc7–Reg1 Phosphatase Signals to Yck1,2 Casein Kinase 1 to Regulate Transport Activity and Glucose-Induced Inactivation of Saccharomyces Maltose Permease
Authors: Gadura Nidhi , Robinson Lucy C , Michels Corinne A 
Published: December 2005

Abstract
The Saccharomyces casein kinase 1 isoforms encoded by the essential gene pair YCK1 and YCK2 control cell growth and morphogenesis and are linked to the endocytosis of several membrane proteins. Here we define roles for the Yck1,2 kinases in Mal61p maltose permease activation and trafficking, using a yck1Δ yck2-2ts (yckts) strain with conditional Yck activity. Moreover, we provide evidence that Glc7–Reg1 phosphatase acts as an upstream activator of Yck1,2 kinases in a novel signaling pathway that modulates kinase activity in response to carbon source availability. The yckts strain exhibits significantly reduced maltose transport activity despite apparently normal levels and cell surface localization of maltose permease protein. Glucose-induced internalization and rapid loss of maltose transport activity of Mal61/HAp-GFP are not observed in the yckts strain and maltose permease proteolysis is blocked. We show that a reg1Δ mutant exhibits a phenotype remarkably similar to that conferred by yckts. The reg1Δ phenotype is not enhanced in the yckts reg1Δ double mutant and is suppressed by increased Yck1,2p dosage. Further, although Yck2p localization and abundance do not change in the reg1Δ mutant, Yck1,2 kinase activity, as assayed by glucose-induced HXT1 expression and Mth1 repressor stability, is substantially reduced in the reg1Δ strain.
The Integral Membrane Protein Pom34p Functionally Links Nucleoporin Subcomplexes
Authors: Miao Mi , Ryan Kathryn J , Wente Susan R 
Published: December 2005

Abstract
Here we have examined the function of Pom34p, a novel membrane protein in Saccharomyces cerevisiae, localized to nuclear pore complexes (NPCs). Membrane topology analysis revealed that Pom34p is a double-pass transmembrane protein with both the amino (N) and carboxy (C) termini positioned on the cytosolic/pore face. The network of genetic interactions between POM34 and genes encoding other nucleoporins was established and showed specific links between Pom34p function and Nup170p, Nup188p, Nup59p, Gle2p, Nup159p, and Nup82p. The transmembrane domains of Pom34p in addition to either the N- or C-terminal region were necessary for its function in different double mutants. We further characterized the pom34ΔN nup188Δ mutant and found it to be perturbed in both NPC structure and function. Mislocalization of a subset of nucleoporins harboring phenylalanine–glycine repeats was observed, and nuclear import capacity for the Kap104p and Kap121p pathways was inhibited. In contrast, the pom34Δ pom152Δ double mutant was viable at all temperatures and showed no such defects. Interestingly, POM152 overexpression suppressed the synthetic lethality of pom34Δ nup170Δ and pom34Δ nup59Δ mutants. We speculate that multiple integral membrane proteins, either within the nuclear pore domain or in the nuclear envelope, execute coordinated roles in NPC structure and function.
Analysis of Pyrimidine Catabolism inDrosophila melanogasterUsing Epistatic Interactions With Mutations of Pyrimidine Biosynthesis and β-Alanine Metabolism
Authors: Rawls John M 
Published: December 2005

AbstractThe biochemical pathway for pyrimidine catabolism links the pathways for pyrimidine biosynthesis and salvage with β-alanine metabolism, providing an array of epistatic interactions with which to analyze mutations of these pathways. Loss-of-function mutations have been identified and characterized for each of the enzymes for pyrimidine catabolism: dihydropyrimidine dehydrogenase (DPD), su(r) mutants; dihydropyrimidinase (DHP), CRMP mutants; β-alanine synthase (βAS), pyd3 mutants. For all three genes, mutants are viable and fertile and manifest no obvious phenotypes, aside from a variety of epistatic interactions. Mutations of all three genes disrupt suppression by the rudimentary gain-of-function mutation (rSu(b)) of the dark cuticle phenotype of black mutants in which β-alanine pools are diminished; these results confirm that pyrimidines are the major source of β-alanine in cuticle pigmentation. The truncated wing phenotype of rudimentary mutants is suppressed completely by su(r) mutations and partially by CRMP mutations; however, no suppression is exhibited by pyd3 mutations. Similarly, su(r) mutants are hypersensitive to dietary 5-fluorouracil, CRMP mutants are less sensitive, and pyd3 mutants exhibit wild-type sensitivity. These results are discussed in the context of similar consequences of 5-fluoropyrimidine toxicity and pyrimidine catabolism mutations in humans.
Genomewide Screen Reveals a Wide Regulatory Network for Di/Tripeptide Utilization inSaccharomyces cerevisiae
Authors: Cai Houjian , Kauffman Sarah , Naider Fred , Becker Jeffrey M 
Published: December 2005

AbstractSmall peptides of two to six residues serve as important sources of amino acids and nitrogen required for growth by a variety of organisms. In the yeast Saccharomyces cerevisiae, the membrane transport protein Ptr2p, encoded by PTR2, mediates the uptake of di/tripeptides. To identify genes involved in regulation of dipeptide utilization, we performed a systematic, functional examination of this process in a haploid, nonessential, single-gene deletion mutant library. We have identified 103 candidate genes: 57 genes whose deletion decreased dipeptide utilization and 46 genes whose deletion enhanced dipeptide utilization. On the basis of Ptr2p-GFP expression studies, together with PTR2 expression analysis and dipeptide uptake assays, 42 genes were ascribed to the regulation of PTR2 expression, 37 genes were involved in Ptr2p localization, and 24 genes did not apparently affect Ptr2p-GFP expression or localization. The 103 genes regulating dipeptide utilization were distributed among most of the Gene Ontology functional categories, indicating a very wide regulatory network involved in transport and utilization of dipeptides in yeast. It is anticipated that further characterization of how these genes affect peptide utilization should add new insights into the global mechanisms of regulation of transport systems in general and peptide utilization in particular.
Goldfish Hematopoietic Necrosis Herpesvirus (Cyprinid Herpesvirus 2) in the USA: Molecular Confirmation of Isolates from Diseased Fish
Authors: Goodwin A. E. , Khoo L. , LaPatra S. E. , Bonar C. , Key D. W. , Garner M. , Lee M. V. , Hanson L. 
Published: December 2005

Abstract
Moribund goldfish Carassius auratus from private collections and breeding facilities were tested for hematopoietic necrosis herpesvirus 2 (also known as cyprinid herpesvirus 2 (CyHV-2)) by degenerate polymerase chain reaction (PCR) of the viral polymerase gene followed by sequencing. The degenerate PCR method produced a fragment with a DNA sequence that was more than 99% identical to the sequence of CyHV-2. Histology and electron microscopy showed that the moribund fish had severe necrosis in the hematopoietic tissues of the kidney and spleen and that herpesvirus particles were present. In the three cases studied, the presence of the virus was associated with high mortality (up to 80%) that could not be attributed to any other cause. The CyHV-2 is very difficult to isolate in cell culture, but our PCR and case studies demonstrate that this virus has a wide geographic distribution in the United States and that goldfish hematopoietic necrosis herpesvirus disease is likely to be an important, but rarely detected, disease of goldfish.
Comparison of Different Monitoring Programs of the 2002 Summer Flood in the River Elbe
Authors: Baborowski Martina , Claus Evelyn , Friese Kurt , von der Kammer Frank , Kasimir Petra , Pelzer Jürgen , Heininger Peter 
Published: December 2005

AbstractThe water quality of the river Elbe near Magdeburg represents the pollution situation of the middle course of the river Elbe under normal discharge conditions. In order to identify critical changes in the water quality caused by the century flood in August 2002, numerous measurement programs were launched accompanying the flood wave. This paper compares and discusses results based on different sampling strategies and analytical methods of three institutions mainly using the example of trace metals.
Assessing the Pollution of Water Protection Areas and River Banks along the Elbe and Mulde Rivers after the Flood Event in August 2002
Authors: Strauch Gerhard , Bittkau Anke , Schlosser Dietmar , Petzoldt Heike , Sbjeschnid André 
Published: December 2005

AbstractInvestigations addressing the pollution with inorganic and potentially pathogenic contaminants resulting from the August 2002 high flood event of the rivers Elbe and Mulde have been performed in water protection areas and along the inundated banks of both rivers. Soil and plant material were investigated for potential pathogens and indicator organisms such as coliforms, Escherichia coli, enterococci, Clostridium perfringens, Pseudomonas aeruginosa, and for inorganic compounds like Al, Zn, nitrate, and orthophosphate. Soil sediments down to a depth of 120 cm, as well as soils and plants along traverses have extensively been studied over a time range of up to one year after the flood event but in none of these environmental compartments a significant maintenance of pollutants could be proven. However, recommendations are given concerning the assessment of microbiological contamination that may arise from possible future flood events.
Ecotoxicological Profiling of Transect River Elbe Sediments
Authors: Grote Matthias , Altenburger Rolf , Brack Werner , Moschütz Susanne , Mothes Sibylle , Michael Claudia , Narten Gesa‐Britt , Paschke Albrecht , Schirmer Kristin , Walter Helge , Wennrich Rainer , Wenzel Klaus‐Dieter , Schüürmann Gerrit 
Published: December 2005

AbstractDuring the river Elbe flood in August 2002, large amounts of suspended organic matter were transported and settled in the course of the river. The aim of this study was to assess the quality of river Elbe sediments using chemical and biological methods. For this purpose 11 samples from river Elbe and 2 from tributaries were investigated. Two contact biotest systems, used to identify the ecotoxic potential of sediments, showed toxic effects in all sediments. Exposure was assessed by quantification of priority pollutants; however, no causal link to biological effects could be established. Effect qualities were characterised by testing organic sediment extracts in a biotest battery consisting of 8 test systems. Test systems varied in sensitivity to detect effects in the samples. Furthermore, samples differed in their ecotoxic potential. An effect‐directed analysis was conducted in order to identify compounds responsible for the biological effects. Cause‐effect relationships were established for mixtures of polycyclic aromatic hydrocarbons being partially responsible for toxic effects on algal reproduction; however the majority of the cause for toxicity remained unclear. Overall, it has to be concluded that Elbe sediments are not in accord with current quality goals. The chemical and the biological transect profile of the sediments indicate toxicant inputs from Czech Republic, river Mulde and diverse source.
Multitemporal and Multispectral Remote Sensing Approach for Flood Detection in the Elbe‐Mulde Region 2002
Authors: Gläßer Cornelia , Reinartz Peter 
Published: December 2005

AbstractThe extreme flood event of the Elbe and Mulde Rivers in August 2002 caused, with its very sharp rise and decline of the water masses, a manifold of damage to the infrastructure as well as toxic deposits in the flooded areas. The paper gives a summary of the processing of multitemporal and multisensor remote sensing data for the purpose of monitoring this event. Methods and results for several thematic questions are presented and discussed. Procedures for the detection of flooded areas with operational satellite data (Landsat‐7 ETM, IRS) are investigated. Further studies are performed regarding the classification of moisture classes in the flood plain in relation to the high water changes, the accumulation of sediments and silts for different land use classes and the erosive impact of the flood by using data with high spatial resolution from satellite (IKONOS) and from aircraft (Daedalus‐Scanner).The time series of multispectral scanner data are very well suited for the spatial analysis of the damage and ecological risk, caused by the flood. The results correlate well with the data from in‐situ measurements. At the same time they show how the gathering of samples can be optimized by using remote sensing data. The results can be directly integrated in existing GIS of the public authorities for the assessment and management of extreme flood events.