bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the Cell Adhesion Molecule Sticks-and-Stones Reveals Multiple Redundant Functional Domains, Protein-Interaction Motifs and Phosphorylated Tyrosines That Direct Myoblast Fusion in Drosophila melanogaster
Authors: Kocherlakota Kiranmai S , Wu Jian-min , McDermott Jeffrey , Abmayr Susan M 
Published: February 2008

Abstract
The larval body wall muscles of Drosophila melanogaster arise by fusion of founder myoblasts (FMs) and fusion-competent myoblasts (FCMs). Sticks-and-Stones (SNS) is expressed on the surface of all FCMs and mediates adhesion with FMs and developing syncytia. Intracellular components essential for myoblast fusion are then recruited to these adhesive contacts. In the studies herein, a functional analysis of the SNS cytodomain using the GAL4/UAS system identified sequences that direct myoblast fusion, presumably through recruitment of these intracellular components. An extensive series of deletion and site-directed mutations were evaluated for their ability to rescue the myoblast fusion defects of sns mutant embryos. Deletion studies revealed redundant functional domains within SNS. Surprisingly, highly conserved consensus sites for binding post-synaptic density-95/discs large/zonula occludens-1-domain-containing (PDZ) proteins and serines with a high probability of phosphorylation play no significant role in myoblast fusion. Biochemical studies establish that the SNS cytodomain is phosphorylated at multiple tyrosines and their site-directed mutagenesis compromises the ability of the corresponding transgenes to rescue myoblast fusion. Similar mutagenesis revealed a requirement for conserved proline-rich regions. This complexity and redundancy of multiple critical sequences within the SNS cytodomain suggest that it functions through a complex array of interactions that likely includes both phosphotyrosine-binding and SH3-domain-containing proteins.
Selection in the Making: A Worldwide Survey of Haplotypic Diversity Around a Causative Mutation in Porcine IGF2
Authors: Ojeda A , Huang L-S , Ren J , Angiolillo A , Cho I-C , Soto H , Lemús-Flores C , Makuza S M , Folch J M , Pérez-Enciso M 
Published: February 2008

Abstract
Domestic species allow us to study dramatic evolutionary changes at an accelerated rate due to the effectiveness of modern breeding techniques and the availability of breeds that have undergone distinct selection pressures. We present a worldwide survey of haplotype variability around a known causative mutation in porcine gene IGF2, which increases lean content. We genotyped 34 SNPs spanning 27 kb in 237 domestic pigs and 162 wild boars. Although the selective process had wiped out variability for at least 27 kb in the haplotypes carrying the mutation, there was no indication of an overall reduction in genetic variability of international vs. European local breeds; there was also no evidence of a reduction in variability caused by domestication. The haplotype structure and a plot of Tajima's D against the frequency of the causative mutation across breeds suggested a temporal pattern, where each breed corresponded to a different selective stage. This was observed comparing the haplotype neighbor-joining (NJ) trees of breeds that have undergone increasing selection pressures for leanness, e.g., European local breeds vs. Pietrain. These results anticipate that comparing current domestic breeds will decisively help to recover the genetic history of domestication and contemporary selective processes.
Defining Regions and Rearrangements of the Silene latifolia Y Chromosome
Authors: Bergero R , Charlesworth D , Filatov D A , Moore R C 
Published: February 2008

Abstract
We combine data from published marker genotyping of three sets of S. latifolia Y chromosome deletion mutants with changed sex phenotypes and add genotypes for several new genic markers to refine the deletion map of the Y chromosome and compare it with the X chromosome genetic map. We conclude that the Y chromosome of this species has been derived through multiple rearrangements of the ancestral gene arrangement and that none of the rearrangements so far detected was involved in stopping X–Y recombination. Different Y genotypes may also differ in their gene content and possibly arrangements, suggesting that mapping the Y-linked sex-determining genes will be difficult, even if many further genic markers are obtained. Even in determining the map of Y chromosome markers to discover all the rearrangements, physical mapping by FISH or other experiments will be essential. Future deletion mapping work should ensure that markers are studied in the parents of deletion mutants and should probably include additional deletions that were not ascertained by causing mutant sex phenotypes.
Characterization of Quantitative Trait Loci Controlling Genetic Variation for Preharvest Sprouting in Synthetic Backcross-Derived Wheat Lines
Authors: Imtiaz Muhammad , Ogbonnaya Francis C , Oman Jason , van Ginkel Maarten 
Published: February 2008

Abstract
Aegilops tauschii, the wild relative of wheat, has stronger seed dormancy, a major component of preharvest sprouting resistance (PHSR), than bread wheat. A diploid Ae. tauschii accession (AUS18836) and a tetraploid (Triticum turgidum L. ssp. durum var. Altar84) wheat were used to construct a synthetic wheat (Syn37). The genetic architecture of PHS was investigated in 271 BC1F7 synthetic backcross lines (SBLs) derived from Syn37/2*Janz (resistant/susceptible). The SBLs were evaluated in three environments over 2 years and PHS was assessed by way of three measures: the germination index (GI), which measures grain dormancy, the whole spike assay (SI), which takes into account all spike morphology, and counted visually sprouted seeds out of 200 (VI). Grain color was measured using both Chroma Meter- and NaOH-based approaches. QTL for PHSR and grain color were mapped and their additive and epistatic effects as well as their interactions with environment were estimated by a mixed linear-model approach. Single-locus analysis following composite interval mapping revealed four QTL for GI, two QTL for SI, and four QTL for VI on chromosomes 3DL and 4AL. The locus QPhs.dpiv-3D.1 on chromosome 3DL was tightly linked to the red grain color (RGC) at a distance of 5 cM. The other locus on chromosome 3D, “QPhs.dpiv-3D.2” was independent of RGC locus. Two-locus analysis detected nine QTL with main effects and 18 additive × additive interactions for GI, SI, and VI. Two of the nine main effects QTL and two epistatic QTL showed significant interactions with environments. Both additive and epistatic effects contributed to phenotypic variance in PHSR and the identified markers are potential candidates for marker-assisted selection of favorable alleles at multiple loci. SBLs derived from Ae. tauschii proved to be a promising tool to dissect, introgress, and pyramid different PHSR genes into adapted wheat genetic backgrounds. The enhanced expression of PHS resistance in SBLs enabled us to develop white PHS-resistant wheat germplasm from the red-grained Ae. tauschii accession.
Genetic Analysis of the Role of Peroxisomes in the Utilization of Acetate and Fatty Acids in Aspergillus nidulans
Authors: Hynes Michael J , Murray Sandra L , Khew Gillian S , Davis Meryl A 
Published: February 2008

Abstract
Peroxisomes are organelles containing a diverse array of enzymes. In fungi they are important for carbon source utilization, pathogenesis, development, and secondary metabolism. We have studied Aspergillus nidulans peroxin (pex) mutants isolated by virtue of their inability to grow on butyrate or by the inactivation of specific pex genes. While all pex mutants are able to form colonies, those unable to import PTS1 proteins are partially defective in asexual and sexual development. The pex mutants are able to grow on acetate but are affected in growth on fatty acids, indicating a requirement for the peroxisomal localization of β-oxidation enzymes. However, mislocalization of malate synthase does not prevent growth on either fatty acids or acetate, showing that the glyoxylate cycle does not require peroxisomal localization. Proliferation of peroxisomes is dependent on fatty acids, but not on acetate, and on PexK (Pex11), expression of which is activated by the FarA transcription factor. Proliferation was greatly reduced in a farAΔ strain. A mutation affecting a mitochodrial ketoacyl-CoA thiolase and disruption of a mitochondrial hydroxy-acyl-CoA dehydrogenase gene prevented growth on short-chain but not long-chain fatty acids. Together with previous results, this is consistent with growth on even-numbered short-chain fatty acids requiring a mitochondrial as well as a peroxisomal β-oxidation pathway. The mitochondrial pathway is not required for growth on valerate or for long-chain fatty acid utilization.
Multilocus Patterns of Polymorphism and Selection Across the X Chromosome of Caenorhabditis remanei
Authors: Cutter Asher D 
Published: February 2008

Abstract
Natural selection and neutral processes such as demography, mutation, and gene conversion all contribute to patterns of polymorphism within genomes. Identifying the relative importance of these varied components in evolution provides the principal challenge for population genetics. To address this issue in the nematode Caenorhabditis remanei, I sampled nucleotide polymorphism at 40 loci across the X chromosome. The site-frequency spectrum for these loci provides no evidence for population size change, and one locus presents a candidate for linkage to a target of balancing selection. Selection for codon usage bias leads to the non-neutrality of synonymous sites, and despite its weak magnitude of effect (Nes ∼0.1), is responsible for profound patterns of diversity and divergence in the C. remanei genome. Although gene conversion is evident for many loci, biased gene conversion is not identified as a significant evolutionary process in this sample. No consistent association is observed between synonymous-site diversity and linkage-disequilibrium-based estimators of the population recombination parameter, despite theoretical predictions about background selection or widespread genetic hitchhiking, but genetic map-based estimates of recombination are needed to rigorously test for a diversity–recombination relationship. Coalescent simulations also illustrate how a spurious correlation between diversity and linkage-disequilibrium-based estimators of recombination can occur, due in part to the presence of unbiased gene conversion. These results illustrate the influence that subtle natural selection can exert on polymorphism and divergence, in the form of codon usage bias, and demonstrate the potential of C. remanei for detecting natural selection from genomic scans of polymorphism.
The ATG12-Conjugating Enzyme ATG10 Is Essential for Autophagic Vesicle Formation in Arabidopsis thaliana
Authors: Phillips Allison R , Suttangkakul Anongpat , Vierstra Richard D 
Published: February 2008

Abstract
Autophagy is an important intracellular recycling system in eukaryotes that utilizes small vesicles to traffic cytosolic proteins and organelles to the vacuole for breakdown. Vesicle formation requires the conjugation of the two ubiquitin-fold polypeptides ATG8 and ATG12 to phosphatidylethanolamine and the ATG5 protein, respectively. Using Arabidopsis thaliana mutants affecting the ATG5 target or the ATG7 E1 required to initiate ligation of both ATG8 and ATG12, we previously showed that the ATG8/12 conjugation pathways together are important when plants encounter nutrient stress and during senescence. To characterize the ATG12 conjugation pathway specifically, we characterized a null mutant eliminating the E2-conjugating enzyme ATG10 that, similar to plants missing ATG5 or ATG7, cannot form the ATG12-ATG5 conjugate. atg10-1 plants are hypersensitive to nitrogen and carbon starvation and initiate senescence and programmed cell death (PCD) more quickly than wild type, as indicated by elevated levels of senescence- and PCD-related mRNAs and proteins during carbon starvation. As detected with a GFP-ATG8a reporter, atg10-1 and atg5-1 mutant plants fail to accumulate autophagic bodies inside the vacuole. These results indicate that ATG10 is essential for ATG12 conjugation and that the ATG12-ATG5 conjugate is necessary to form autophagic vesicles and for the timely progression of senescence and PCD in plants.
Genomic Organization, Rapid Evolution and Meiotic Instability of Nucleotide-Binding-Site-Encoding Genes in a New Fruit Crop, “Chestnut Rose”
Authors: Xu Qiang , Wen Xiaopeng , Deng Xiuxin 
Published: February 2008

Abstract
From chestnut rose, a promising fruit crop of the Rosa genus, powdery mildew disease-resistant and susceptible genotypes and their F1 progeny were used to isolate nucleotide-binding-site (NBS)-encoding genes using 19 degenerate primer pairs and an additional cloning method called overlapping extension amplification. A total of 126 genes were harvested; of these, 38 were from a resistant parent, 37 from a susceptible parent, and 51 from F1 progeny. A phylogenetic tree was constructed, which revealed that NBS sequences from parents and F1 progeny tend to form a mixture and are well distributed among the branches of the tree. Mapping of these NBS genes suggested that their organization in the genome is a “tandem duplicated cluster” and, to a lesser extent, a “heterogeneous cluster.” Intraspecific polymorphisms and interspecific divergence were detected by Southern blotting with NBS-encoding genes as probes. Sequencing on the nucleotide level revealed even more intraspecific variation: for the R4 gene, 9.81% of the nucleotides are polymorphic. Amino acid sites under positive selection were detected in the NBS region. Some NBS-encoding genes were meiotically unstable, which may due to recombination and deletion events. Moreover, a transposon-like element was isolated in the flanking region of NBS genes, implying a possible role for transposon in the evolutionary history of resistance genes.
Early Gene Duplication Within Chloroplastida and Its Correspondence With Relocation of Starch Metabolism to Chloroplasts
Authors: Deschamps Philippe , Moreau Hervé , Worden Alexandra Z , Dauvillée David , Ball Steven G 
Published: February 2008

Abstract
The endosymbiosis event resulting in the plastid of photosynthetic eukaryotes was accompanied by the appearance of a novel form of storage polysaccharide in Rhodophyceae, Glaucophyta, and Chloroplastida. Previous analyses indicated that starch synthesis resulted from the merging of the cyanobacterial and the eukaryotic storage polysaccharide metabolism pathways. We performed a comparative bioinformatic analysis of six algal genome sequences to investigate this merger. Specifically, we analyzed two Chlorophyceae, Chlamydomonas reinhardtii and Volvox carterii, and four Prasinophytae, two Ostreococcus strains and two Micromonas pusilla strains. Our analyses revealed a complex metabolic pathway whose intricacies and function seem conserved throughout the green lineage. Comparison of this pathway to that recently proposed for the Rhodophyceae suggests that the complexity that we observed is unique to the green lineage and was generated when the latter diverged from the red algae. This finding corresponds well with the plastidial location of starch metabolism in Chloroplastidae. In contrast, Rhodophyceae and Glaucophyta produce and store starch in the cytoplasm and have a lower complexity pathway. Cytoplasmic starch synthesis is currently hypothesized to represent the ancestral state of storage polysaccharide metabolism in Archaeplastida. The retargeting of components of the cytoplasmic pathway to plastids likely required a complex stepwise process involving several rounds of gene duplications. We propose that this relocation of glucan synthesis to the plastid facilitated evolution of chlorophyll-containing light-harvesting complex antennae by playing a protective role within the chloroplast.
Effective Fennel (Foeniculum vulgare) Control with Herbicides in Natural Habitats in California
Authors: Bell Carl E. , Easley Todd , Goodman Kari Roesch 
Published: February 2008

AbstractFennel is a major invasive plant in many lower elevation natural areas in coastal California. Three identical field experiments were conducted to evaluate glyphosate and triclopyr for control of fennel. Treatments included each herbicide applied alone and in various combinations. We also compared broadcast applications to spot spraying of individual fennel plants because spot spraying is a commonly used technique in natural area weed management. Most treatments controlled fennel well when evaluated 6 wk and 1 yr after treatment, with the exception of the lowest rate of glyphosate. Purple needlegrass, a native perennial grass, was present in two of the sites. In most, but not all, treatment and site combinations, it was not significantly harmed by the herbicides. The spot spray applications were less effective and used more herbicide per unit area than the broadcast spraying.
Integrated Management of Perennial Pepperweed (Lepidium latifolium)
Authors: Wilson Rob G. , Boelk Debra , Kyser Guy B. , DiTomaso Joseph M. 
Published: February 2008

AbstractPerennial pepperweed is invasive throughout California. It thrives in a wide range of environments and is a common weed in floodplains, pastures, wetlands, and roadsides. In disturbed areas, perennial pepperweed rapidly forms monotypic stands with a thick litter layer. These infestations not only out-compete other vegetation, but prevent re-establishment of desirable species even after perennial pepperweed control. This experiment examined integrated management strategies with the goal of maximizing perennial pepperweed control and establishment of desirable native vegetation. The experiment was conducted at two sites in Lassen County, CA. Both sites were heavily infested with perennial pepperweed and lacked competing vegetation. The experimental design was a split-split-randomized block with four replications. Site preparation treatments included winter burning, summer and fall mowing, winter grazing, and fall disking. These treatments were designed to remove thatch to facilitate herbicide application and reseeding of desirable perennial grasses. Herbicide treatments included chlorsulfuron, 2,4-D, or glyphosate applied at the flower bud stage. Revegetation treatments included no seeding and no-till seeding of native perennial grasses. Most site preparation plus herbicide combinations reduced perennial pepperweed cover > 85% compared to the untreated control, although treatment efficacy was variable between sites and years. Burning, grazing, mowing, or disking in combination with herbicide treatment and no-till seeding was necessary for successful native perennial grass establishment. Burning or mowing with yearly 2,4-D applications for 3 yr gave the best combination of perennial pepperweed control and native grass establishment. Chlorsulfuron caused chlorosis and stunting to western wheatgrass, basin wildrye, and beardless wildrye at both sites when applied the spring before seeding. No treatment offered complete weed control, suggesting follow-up spot herbicide applications are needed for long-term perennial pepperweed suppression. These results provide several successful integrated strategies for control of perennial pepperweed and revegetation to a desired native perennial grass community.
Medusahead (Taeniatherum caput-medusae) Outperforms Squirreltail (Elymus elymoides) through Interference and Growth Rate
Authors: Young K. , Mangold J. 
Published: February 2008

AbstractUnderstanding the ecological processes that foster invasion and dominance by medusahead is central to its management. The objectives of this study were (1) to quantify and compare interference between medusahead and squirreltail under different concentrations of soil nitrogen (N) and phosphorous (P) and (2) to compare growth rates of medusahead and squirreltail under field soil N and P availabilities. We grew medusahead and squirreltail in an addition series in a greenhouse and applied one of four nutrient treatments weekly: (1) low N low P (no N or P added), (2) low N high P (added 250 ml of 600 µM P solution in the form of calcium phosphate), (3) high N low P (added 250 ml of 8,400 µM N solution in the forms of calcium nitrate and potassium nitrate), and (4) high N high P (added solutions as listed above for high N and high P). After 70 d density and biomass by species were sampled. We also grew individual medusahead and squirreltail plants in control soil conditions. Biomass, leaf area, and root length were determined for each species at 14-d intervals over 72 d. Regression models for medusahead and squirreltail suggested N appeared to be playing a much larger role than P in interference between the species. The high N treatment did not increase medusahead's interference ability relative to squirreltail as we had hypothesized. Medusahead typically imposed a two-to-seven-times stronger influence on interference relationships than squirreltail. Medusahead accumulated biomass, leaf area, and root length twice as fast as squirreltail. Results from our study suggest that medusahead seedlings will likely dominate over squirreltail seedlings. To restore squirreltail to medusahead-infested rangeland, medusahead densities should be reduced with integrated weed management strategies. On medusahead-free rangeland, prevention and early detection and eradication programs are critical.
The Estes Valley, Colorado: A Case Study of a Weed Management Area
Authors: Gunderson-Izurieta Sharlyn , Paulson Deborah , Enloe Stephen F. 
Published: February 2008

AbstractWeed Management Areas (WMAs) are an important approach for managing invasive plants. However, most WMAs are relatively recent, and little is known about how these active partnerships can be maintained over the long term. This case study of the Estes Valley WMA examined the early community support that led to the establishment of a WMA and reasons why the Estes Valley WMA did not continue as a collaborative process. The analysis uncovered four factors that were critical to the early success of the Estes Valley WMA group: community education/awareness, key participants, a community sense of responsibility, and economic/aesthetic values. The analysis also uncovered four factors explaining why the Estes Valley WMA did not continue: a lack of group structure, unclear boundary definitions, availability of funding, and decline in motivation. Residents of the Estes Valley now rely more on the county and private contractors to provide weed management services. While this approach is meeting basic weed management needs, some interviewees feel that community involvement has declined. Recommendations are given for the reestablishment of a collaborative weed management group in the Estes Valley.