bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of Mixed-Model Approaches for Association Mapping
Authors: Stich Benjamin , Möhring Jens , Piepho Hans-Peter , Heckenberger Martin , Buckler Edward S , Melchinger Albrecht E
Published: February 2008

Association-mapping methods promise to overcome the limitations of linkage-mapping methods. The main objectives of this study were to (i) evaluate various methods for association mapping in the autogamous species wheat using an empirical data set, (ii) determine a marker-based kinship matrix using a restricted maximum-likelihood (REML) estimate of the probability of two alleles at the same locus being identical in state but not identical by descent, and (iii) compare the results of association-mapping approaches based on adjusted entry means (two-step approaches) with the results of approaches in which the phenotypic data analysis and the association analysis were performed in one step (one-step approaches). On the basis of the phenotypic and genotypic data of 303 soft winter wheat (Triticum aestivum L.) inbreds, various association-mapping methods were evaluated. Spearman's rank correlation between P-values calculated on the basis of one- and two-stage association-mapping methods ranged from 0.63 to 0.93. The mixed-model association-mapping approaches using a kinship matrix estimated by REML are more appropriate for association mapping than the recently proposed QK method with respect to (i) the adherence to the nominal α-level and (ii) the adjusted power for detection of quantitative trait loci. Furthermore, we showed that our data set could be analyzed by using two-step approaches of the proposed association-mapping method without substantially increasing the empirical type I error rate in comparison to the corresponding one-step approaches.
MultivariateQst–Fst Comparisons: A Neutrality Test for the Evolution of the G Matrix in Structured Populations
Authors: Martin Guillaume , Chapuis Elodie , Goudet Jérôme
Published: February 2008

Neutrality tests in quantitative genetics provide a statistical framework for the detection of selection on polygenic traits in wild populations. However, the existing method based on comparisons of divergence at neutral markers and quantitative traits (Qst–Fst) suffers from several limitations that hinder a clear interpretation of the results with typical empirical designs. In this article, we propose a multivariate extension of this neutrality test based on empirical estimates of the among-populations (D) and within-populations (G) covariance matrices by MANOVA. A simple pattern is expected under neutrality: D = 2Fst/(1 − Fst)G, so that neutrality implies both proportionality of the two matrices and a specific value of the proportionality coefficient. This pattern is tested using Flury's framework for matrix comparison [common principal-component (CPC) analysis], a well-known tool in G matrix evolution studies. We show the importance of using a Bartlett adjustment of the test for the small sample sizes typically found in empirical studies. We propose a dual test: (i) that the proportionality coefficient is not different from its neutral expectation [2Fst/(1 − Fst)] and (ii) that the MANOVA estimates of mean square matrices between and among populations are proportional. These two tests combined provide a more stringent test for neutrality than the classic Qst–Fst comparison and avoid several statistical problems. Extensive simulations of realistic empirical designs suggest that these tests correctly detect the expected pattern under neutrality and have enough power to efficiently detect mild to strong selection (homogeneous, heterogeneous, or mixed) when it is occurring on a set of traits. This method also provides a rigorous and quantitative framework for disentangling the effects of different selection regimes and of drift on the evolution of the G matrix. We discuss practical requirements for the proper application of our test in empirical studies and potential extensions.
Functioning of the Drosophila Wilms'-Tumor-1-Associated Protein Homolog, Fl(2)d, in Sex-Lethal-Dependent Alternative Splicing
Authors: Penn Jill K M , Graham Patricia , Deshpande Girish , Calhoun Gretchen , Chaouki Ahmad Sami , Salz Helen K , Schedl Paul
Published: February 2008

fl(2)d, the Drosophila homolog of Wilms'-tumor-1-associated protein (WTAP), regulates the alternative splicing of Sex-lethal (Sxl), transformer (tra), and Ultrabithorax (Ubx). Although WTAP has been found in functional human spliceosomes, exactly how it contributes to the splicing process remains unknown. Here we attempt to identify factors that interact genetically and physically with fl(2)d. We begin by analyzing the Sxl-Fl(2)d protein–protein interaction in detail and present evidence suggesting that the female-specific fl(2)d1 allele is antimorphic with respect to the process of sex determination. Next we show that fl(2)d interacts genetically with early acting general splicing regulators and that Fl(2)d is present in immunoprecipitable complexes with Snf, U2AF50, U2AF38, and U1-70K. By contrast, we could not detect Fl(2)d complexes containing the U5 snRNP protein U5-40K or with a protein that associates with the activated B spliceosomal complex SKIP. Significantly, the genetic and molecular interactions observed for Sxl are quite similar to those detected for fl(2)d. Taken together, our findings suggest that Sxl and fl(2)d function to alter splice-site selection at an early step in spliceosome assembly.
Independent Effects of cis- and trans-regulatory Variation on Gene Expression in Drosophila melanogaster
Authors: Wittkopp Patricia J , Haerum Belinda K , Clark Andrew G
Published: February 2008

Biochemical interactions between cis-regulatory DNA sequences and trans-regulatory gene products suggest that cis- and trans-acting polymorphisms may interact genetically. Here we present a strategy to test this hypothesis by comparing the relative cis-regulatory activity of two alleles in different genetic backgrounds. Of the eight genes surveyed in this study, five were affected by trans-acting variation that altered total transcript levels, two of which were also affected by differences in cis-regulation. The presence of trans-acting variation had no effect on relative cis-regulatory activity, showing that cis-regulatory polymorphisms can function independently of trans-regulatory variation. The frequency of such independent interactions on a genomic scale is yet to be determined.
Drop-Size Soda Lakes: Transient Microbial Habitats on a Salt-Secreting Desert Tree
Authors: Qvit-Raz Noga , Jurkevitch Edouard , Belkin Shimshon
Published: February 2008

We describe a hitherto unrecognized bacterial community, inhabiting the leaf surfaces of the salt-excreting desert tree Tamarix. High temperatures, strong radiation, and very low humidity dictate a daytime existence in complete desiccation, but damp nights allow the microbial population to proliferate in a sugar-rich, alkaline, and hypersaline solution, before drying up again after sunrise. The exclusively bacterial population contains many undescribed species and genera, but nevertheless appears to be characterized by relatively limited species diversity. Sequences of 16S rRNA genes from either isolates or total community DNA place the identified members of the community in five bacterial groups (Actinobacteria, Bacteroidetes, Firmicutes, α-, and γ-Proteobacteria); in each of these, they concentrate in a very narrow branch that in most cases harbors organisms isolated from unrelated halophilic environments.
Fine Haplotype Structure of a Chromosome 17 Region in the Laboratory and Wild Mouse
Authors: Trachtulec Zdenek , Vlcek Cestmir , Mihola Ondrej , Gregorova Sona , Fotopulosova Vladana , Forejt Jiri
Published: February 2008

Extensive linkage disequilibrium among classical laboratory strains represents an obstacle in the high-resolution haplotype mapping of mouse quantitative trait loci (QTL). To determine the potential of wild-derived mouse strains for fine QTL mapping, we constructed a haplotype map of a 250-kb region of the t-complex on chromosome 17 containing the Hybrid sterility 1 (Hst1) gene. We resequenced 33 loci from up to 80 chromosomes of five mouse (sub)species. Trans-species single-nucleotide polymorphisms (SNPs) were rare between Mus m. musculus (Mmmu) and Mus m. domesticus (Mmd). The haplotypes in Mmmu and Mmd differed and therefore strains from these subspecies should not be combined for haplotype-associated mapping. The haplotypes of t-chromosomes differed from all non-t Mmmu and Mmd haplotypes. Half of the SNPs and SN indels but only one of seven longer rearrangements found in classical laboratory strains were useful for haplotype mapping in the wild-derived M. m. domesticus. The largest Mmd haplotype block contained three genes of a highly conserved synteny. The lengths of the haplotype blocks deduced from 36 domesticus chromosomes were in tens of kilobases, suggesting that the wild-derived Mmd strains are suitable for fine interval-specific mapping.
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

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

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

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

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

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

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

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

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

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

Fennel 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

Perennial 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

Understanding 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

Weed 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.
Jubatagrass (Cortaderia jubata) Control Using Chemical and Mechanical Methods
Authors: DiTomaso Joseph M. , Drewitz Jennifer J. , Kyser Guy B.
Published: February 2008

Jubatagrass is one of the most invasive plants along the California and southern Oregon coast. It establishes dense populations that can severely impact native plant diversity and conifer seedling recruitment following forestry operations. This goal of this study was to evaluate the effectiveness of both manual removal and several herbicide control options and application techniques. In addition, a cost analysis was also conducted for the most successful herbicide control methods. Results demonstrate that mechanical removal through digging is effective, although labor intensive. Among the herbicides tested, glyphosate applied as a high-volume (spray-to-wet) application (0.6% ae) in early summer, low-volume application (2.4% ae) in early summer or fall, and ropewick technique in early summer or fall (> 9.9% ae) all provided ≥ 88% jubatagrass control, but the low-volume treatments were the most cost effective. Although the graminicide sethoxydim at the highest rate (0.36% ai) did not give effective control, fluazifop applied in the fall in a low-volume treatment (0.98% ai) gave 87% control of jubatagrass. Imazapyr gave some level of control but does not appear to provide an economical option for jubatagrass management. Results of this study demonstrate that in addition to the more conventional methods of mechanical removal and spray-to-wet glyphosate (0.6% ae), control of jubatagrass can also be equally or more effective with low-volume and ropewick applications of glyphosate.
Neural network modelling of RC deep beam shear strength
Authors: Yang K.-H. , Ashour A. F. , Song J.-K. , Lee E.-T.
Published: February 2008

A 9 × 18 × 1 feed-forward neural network (NN) model trained using a resilient back-propagation algorithm and early stopping technique is constructed to predict the shear strength of deep reinforced concrete beams. The input layer covering geometrical and material properties of deep beams has nine neurons, and the corresponding output is the shear strength. Training, validation and testing of the developed neural network have been achieved using a comprehensive database compiled from 362 simple and 71 continuous deep beam specimens. The shear strength predictions of deep beams obtained from the developed NN are in better agreement with test results than those determined from strut-and-tie models. The mean and standard deviation of the ratio between predicted capacities using the NN and measured shear capacities are 1·028 and 0·154, respectively, for simple deep beams, and 1·0 and 0·122, respectively, for continuous deep beams. In addition, the trends ascertained from parametric study using the developed NN have a consistent agreement with those observed in other experimental and analytical investigations.
Conserving biodiversity using risk management: hoax or hope
Authors: Hummel Susan , Donovan Geoffrey H , Spies Thomas A , Hemstrom Miles A
Published: February 2008

Biodiversity has been called a form of ecosystem insurance. According to the “insurance hypothesis”, the presence of many species protects against system decline, because builtin redundancies guarantee that some species will maintain key functions even if others fail. The hypothesis might have merit, but calling it “insurance” promotes an ambiguous understanding of risk management strategies and underlying theories of risk. Instead, such redundancy suggests a strategy of diversification. A clearer understanding of risk includes comprehending the important distinction between risk assessment and risk management, acknowledging the existence of undiversifiable risk, and recognizing that risk and uncertainty are not synonymous. A better grasp of risk management will help anyone interested in assessing the merits of different biodiversity conservation strategies. At stake is the adequacy of conservation strategies for mitigating human‐caused biodiversity losses.
Silica: an essential nutrient in wetland biogeochemistry
Authors: Struyf Eric , Conley Daniel J
Published: February 2008

Recent research has emphasized the importance of terrestrial ecosystems in the global biogeochemical cycle of silica (Si). The production, retention, and dissolution of amorphous silica of biological origin in soils and vegetation effectively control terrestrial Si fluxes. However, surprisingly little is known about the role of wetlands in these processes. Wetlands are known hotspots for both nitrogen and phosphorus cycling, and there have been countless studies and numerous reviews on these nutrients worldwide. By bringing together previously scattered results, we show that wetland ecosystems may be as important for Si transport and processing as they are for other important biogeochemical cycles. Yet, the range of studied systems is small and incomplete. This constitutes a serious gap in our understanding of both coastal eutrophication and climate change, issues that are strongly linked to Si biogeochemistry. Ecosystem scientists and wetland biogeochemists around the world need to begin addressing these issues.
Consistent Intrafamilial Transmission of Actinobacillus actinomycetemcomitans Despite Clonal Diversity
Authors: Doğan Başak , Kipalev Arzu Şahan , Ökte Emel , Sultan Nedim , Asikainen Sirkka E.
Published: February 2008

Background: Actinobacillus actinomycetemcomitans is a major pathogen in aggressive periodontitis. Our objectives were to determine the periodontal status and occurrence of A. actinomycetemcomitans in family members of subjects with A. actinomycetemcomitans–positive aggressive periodontitis (AgP) and to evaluate the probability of its intrafamilial transmission.

Methods: Of the 300 subjects screened, 66 (22%) had AgP and A. actinomycetemcomitans. Eleven (probands) of these 66 subjects with AgP met the strict inclusion criteria for the study. The study population consisted of 55 subjects, including probands and their family members (N = 44). Two family groups were formed according to whether the proband was a child (N = 7) or a parent (N = 4). Subgingival samples from all subjects were cultured for A. actinomycetemcomitans, and its clonal types were determined by combining serotype and genotype data for each isolate.

Results: Among 42 dentate family members, 16 (38%) exhibited periodontitis and eight (50%) had AgP. Periodontitis was found in nine of 12 (75%) of the dentate parents and six of 17 (35%) siblings of the child probands. A. actinomycetemcomitans was detected in 16 of 31 (52%) family members, i.e., one parent and at least one sibling in six families. The child probands shared A. actinomycetemcomitans clonal types with their parents in five of six (83%) families and with their siblings in three of six (50%) families. In the four parent–proband families, A. actinomycetemcomitans occurred in two spouses and all nine children. The parent probands shared A. actinomycetemcomitans clonal types with their spouses in both families and with their children in three of four families. In all families, the likelihood of intrafamilial transmission of A. actinomycetemcomitans was statistically significant. Members of most families (eight of 11, 73%) also harbored additional clonal types of A. actinomycetemcomitans.

Conclusion: Parents and siblings of an individual with A. actinomycetemcomitans–positive AgP may have an increased susceptibility to periodontitis and shared and/or other clonal types of oral A. actinomycetemcomitans.
Short‐Term Effects of rhBMP‐2–Enhanced Bone Augmentation Beyond the Skeletal Envelope Within a Titanium Cap in Rabbit Calvarium
Authors: Hasegawa Yasunori , Sato Shuichi , Takayama Tadahiro , Murai Masakazu , Suzuki Naoto , Ito Koichi
Published: February 2008

Background: Recombinant human bone morphogenetic protein (rhBMP)‐2 in a bioabsorbable collagen sponge (ACS) carrier supports significant bone formation. However, histomorphometric data on the augmentation of bone formation beyond the skeletal envelope are insufficient. Our objective was to evaluate the short‐term effects of rhBMP‐2 on bone augmentation beyond the skeletal envelope within a titanium cap in rabbit calvarium.

Methods: Eighteen adult male Japanese white rabbits were used. ACS soak‐loaded with rhBMP‐2 (100, 500, or 1,000 μg/ml) was placed at the calvarium; controls were packed with ACS alone. After 1 month, the animals were euthanized, and histologic sections were prepared. Newly generated tissue and mineralized bone areas were measured histomorphometrically and expressed as percentage ratios of the total submembranous space area.

Results: At all concentrations, a statistically significant difference in the relative height and amount of newly generated tissue was observed between the experimental and control sites. There was a statistically significant difference in the relative amount of mineralized bone between the experimental and control sites in the 1,000‐μg/ml group, but no statistically significant differences were observed in the 100‐μg/ml and 500‐μg/ml groups.

Conclusion: rhBMP‐2/ACS has a short‐term effect on bone augmentation beyond the skeletal envelope within a titanium cap in rabbit calvarium.
One-pot multicomponent synthesis of substituted 5,7-dihydro-1,6-naphthyridines and 5,6,7,8-tetrahydroquinolines
Authors: Yan Chao-Guo , Wang Qi-Fang , Cai Xi-Mei , Sun Jing
Published: February 2008

An one-pot approach was developed for the synthesis of substituted 5,7-dihydro-1,6-naphthyridines and 5,6,7,8-tetrahydroquinolines with moderate to good yields. This pathway is a modified two-step synthesis of Kröhnke pyridine and involves a four-component tandem reaction of N-phenacylpyridinium bromide, aromatic aldehydes, substituted or nitrogen-containing cyclic ketones and a nitrogen source. This multi-component reaction is performed using microwave irradiation heating of the reaction substrates under an environment of NH4OAc/HOAc.
Representations of Women in the Writings of the Intelligentsia in Hashemite Iraq, 1921–1958
Authors: Bashkin Orit
Published: February 2008

This essay examines representations of Iraqi women in the works of poets, novelists, and public intellectuals during the Hashemite period. Defining the functions of women in modern Muslim societies, Iraqi intellectuals sought inspiration in the writings of Egyptian and Turkish writers. I demonstrate, however, that the discourse about women grew more Iraqi-centric in the 1940s and 50s. I also argue that the changes in the representations of women mirrored the radicalization of the Iraqi intelligentsia. While during the interwar period, the conversation about gender roles was mostly conducted among men who debated education, seclusion, and domesticity, after World War II, social democrats, communists, and radical pan-Arabists utilized the mistreatment of women as a way to criticize the Hashemite state. Women affiliated with these groups defined themselves as citizens, rather than national subjects, with equal rights. The discourse also had global aspects, as Iraqi intellectuals appropriated and hybridized colonial perceptions of Muslim women.
Time course of syringomyelia resolution following decompression of Chiari malformation Type I
Authors: Wetjen Nicholas M. , Heiss John D. , Oldfield Edward H.
Published: February 2008

Object

To better understand syrinx pathophysiology, the authors performed a prospective study in which they used findings from serial clinical and magnetic resonance (MR) imaging examinations performed before and after craniocervical decompression to establish the time course of syrinx narrowing.

Methods

Serial clinical examinations and cervical MR imaging were performed in 29 consecutive patients with Chiari malformation Type I (CM-I) and syringomyelia before surgery, 1 week, and 3–6 months after surgery, and then annually. Time to narrowing of the syrinx (> 50% decrease in maximal anteroposterior diameter) following surgery was calculated using the Kaplan–Meier method.

Results

All syringes decreased in diameter and length (number of segments) on MR images at 3–6 months, 1 year, and 2 years or later. The syrinx diameter decreased from 6.9 ± 2.1 mm (mean ± standard deviation) preoperatively to < 1.5 mm at last evaluation (p < 0.0001). The median time to syrinx narrowing was 3.6 months following CM-I decompression (95% confidence interval 3.0–6.5 months). After surgery 94% of patients had improved symptoms, but symptoms resolved incompletely in 68% of patients; 52 and 59% of patients had residual dysesthesias and sensory loss, respectively. Clinical improvement occurred before partial or complete disappearance of the syrinx on MR images. Patient age, duration of symptoms, sex, preoperative syrinx diameter, and length of syrinx were unrelated to time to syrinx narrowing.

Conclusions

Most patients improve after decompression for CM-I, but many have residual symptoms. Syringes may continue to diminish for months to years after surgical decompression. A collapsed syrinx (absence of distention of the spinal cord) indicates that the pathophysiology has been reversed by treatment regardless of the completeness of elimination of the cavity on MR images.
Long-term outcome in children treated for craniopharyngioma with and without radiotherapy
Authors: Lin Lilie L. , Naqa Issam El , Leonard Jeffrey R. , Park Tae Sung , Hollander Abby S. , Michalski Jeff M. , Mansur David B.
Published: February 2008

Object

The authors report the results of surgery alone or in combination with radiotherapy in the management of craniopharyngiomas in children.

Methods

The authors retrospectively reviewed the outcomes in 31 patients treated for craniopharyngiomas at the Department of Radiation Oncology at Washington University in St. Louis and the St. Louis Children's Hospital. The median age at diagnosis was 8.1 years (range 1.1–21 years). Fourteen patients underwent gross-total resection (GTR) with observation, and 6 patients underwent subtotal resection (STR) with observation. Ten patients underwent STR or cyst aspiration followed by external-beam radiotherapy, and 1 patient underwent cyst aspiration followed by intracystic 32P installation.

Results

The median follow-up for all surviving patients was 78.2 months. Overall survival and local control rates at 10 years were 96 and 58%, respectively. One patient died of the disease, and 12 patients had subsequent recurrences. Of those with recurrences, 6 patients had undergone initial STR with observation and 6 had been treated with GTR and observation. The median time to progression was 17.9 months in the patients who underwent limited resection, and 55 months for those who underwent GTR. There were no recurrences in the patients who received radiotherapy at the time of initial diagnosis.

Conclusions

Radiotherapy delivered as part of the initial management of craniopharyngiomas in children or at the time of recurrence provides effective local control.