bluuebunny/crossref_metadata_2025 huggingface dataset:
Measurement of Gmax and Estimation of K of Saturated Clay Using Bender Elements in an Oedometer
Authors: Zeng X , Grolewski B
Published: March 2005

Recent developments in bender element technique have made it possible to determine Gmax and estimate K0 of soils under complex loading conditions. By measuring the shear wave velocities in different shear planes, the cross anisotropy in Gmax of soil induced by axial-symmetric loading can also be determined. The shear wave velocities can also be used to estimate the horizontal earth pressure coefficient at rest K0. This paper reports on an experimental setup that uses bender elements installed in an oedometer to measure shear wave velocities in four shear planes of a saturated clay specimen under different consolidation pressures. The data is used to investigate the cross anisotropy of stiffness in clay due to a K0 stress condition. The measured Gmax is compared with the results from a commonly used empirical formula. The measured shear wave velocities on different shear planes are also used to calculate K0 of clay under different consolidation pressures and compared with results from empirical formulae. The applied stress condition includes loading, unloading, and reloading of up to 22 cycles, thus providing information to study the influence of repeated loading on Gmax and K0 of a saturated clay.
Determination of Multidirectional p-y Curves for Soft Clays
Authors: Mayoral JM , Pestana JM , Seed RB
Published: March 2005

The evaluation of performance of soil-pile-structure systems under seismic loading is one of the most complex problems in earthquake engineering. In the most common methodology, force-displacement curves are used to describe the nonlinear response of discrete soil springs connecting the piles to the “free-field” soil column using the concept of beam on nonlinear Winkler foundation. Although there is a great interest and on-going research to characterize the multi-directional “free-field” soil response, there is a lack of information and experimental data to formulate p-y curves in multi-directional loading conditions. A new testing device was designed and constructed to obtain high quality data to calibrate numerical tools used to evaluate the seismic performance of structures supported on deep foundations in soft clay. A suite of different ground displacement path scenarios observed during recent earthquakes was simulated to assess the effect of displacement history on measured p-y response.
Utilization of Quarry Dust to Improve the Geotechnical Properties of Soils in Highway Construction
Authors: Soosan TG , Sridharan A , Jose BT , Abraham BM
Published: March 2005

Quarries and aggregate crushers are basic requisites for construction industry and quarry dust is a byproduct of rubble crusher units. Geotechnical and mineralogical characterization of quarry dust and its interaction behavior with soils can lead to viable solutions for its large-scale utilization and disposal. The effect of addition of quarry dust on properties of red earth and two different cohesive soils; viz. kaolinite, Cochin marine clay was studied in detail. The results indicate that compaction characteristics and CBR of soils are improved by addition of quarry dust. Problems associated with the construction of highways over clayey subgrade can be reduced significantly by mixing with quarry dust.
Development of a New Hollow Cylinder Triaxial Apparatus for the Study of Expansion Tests in Clay
Authors: Silvestri V , Diab R , Ducharme A
Published: March 2005

This paper presents the use of a new, automated, Hollow Cylinder Triaxial cell (HCTA) for the study of expansion tests in saturated clay. The hollow cylinder cell was developed by modifying a hydraulic triaxial cell, and was adapted to perform cylindrical cavity expansion tests in annular soil specimens, with measurement of excess pore water pressures generated at various radial distances. The apparatus allows one to perform drained and undrained expansion tests, under plane strain or constant axial stress, with the expansion process being either stress-controlled or strain-controlled. The equipment, testing procedures, and analysis of typical undrained expansion tests are discussed.
Sealed Double-Ring Infiltrometers for Estimating Very Low Hydraulic Conductivities
Authors: Neupane D , Bowders JJ , Loehr JE , Bouazza A , Trautwein SJ
Published: March 2005

Sealed, Double-Ring Infiltrometers (SDRIs) are one of the preferred devices to measure infiltration rates of soil liners in the field. Existing SDRIs are well suited for measuring infiltration rates on materials with hydraulic conductivities on the order of 1 × 10−9 m/s. A very low hydraulic conductivity material (<1 × 10−10 m/s), such as low-k asphalt concrete, requires some modifications to the existing SDRI designs. A Constant Head Board (CHB) was designed and employed to replace the commonly used flexible bag to accomplish measurement of very small flow increments. Flow increments as low as 0.05 mL can be effectively measured with this technique enabling field hydraulic conductivities as low as 1 × 10−11 m/s and possibly lower to be estimated in a matter of a day or two. The CHB is reliable, follows existing methods, and can account for the effects of temperature and barometric pressure changes on the flow rate.
Vibratory Plate Loading of Compacted and Instrumented Field Soil Beds
Authors: Mooney MA , Bouton CO
Published: March 2005

Field scale studies of foundation and plate vibrations, particularly in the nonlinear domain, are vital to improving understanding and validating analytical and numerical efforts. This paper describes the development of an experimental program to investigate the dynamic signature of a rigid plate and of the soil during surface plate vibration of compacted soil beds. Nineteen testing sequences were performed on 1.2-m deep prepared soil test beds embedded with miniature triaxial accelerometers. Various vibratory loading frequencies (10–60 Hz) and amplitudes (up to 220 kPa contact stress) were applied via a 0.45-m-diameter plate to the prepared test beds. The paper describes the load testing frame, the preparation of free field partially-saturated sand test beds, and the placement of triaxial accelerometers within the soil. Plate and soil acceleration profiles are presented for the range of applied forcing frequency and amplitude levels involved. The nonlinear soil-compactor system response is analyzed and presented in both the time and frequency domains to present key features observed during testing.
Determination of Surface and Thickness Characteristics of Textured Geomembranes Using Image Analysis
Authors: Yesiller N , Cekic A
Published: March 2005

Image analysis was used to determine surface topography and thickness of textured geomembranes. Images of cross sections (specimen length × thickness) of geomembranes were obtained at 50× magnification using a digital optical microscope. Thickness was determined as the distance between the top and bottom surfaces along an entire cross section. For surface analysis, profiles of top and bottom surfaces were extracted from the cross section images. Amplitude, spatial, hybrid, and functional texture parameters were determined. Tests were conducted on eleven samples of HDPE and LLDPE geomembranes manufactured by co-extrusion and embossing at varying thicknesses. The geomembranes were classified into three texture categories: high, medium, and low. Anisotropy and directionality were observed for all samples to varying degrees between and within manufacturing directions, respectively. Statistical analysis of the results indicated that surface topography of geomembranes could be determined by analyzing one surface of five specimens with 50 mm length. Comparisons were made between image analysis and mechanical tests for core thickness and asperity height. Image analysis and mechanical measurements were significantly different. Recommendations were made for the redesign of the mechanical devices by sizing the components in relation to the size and spacing of geomembrane texture features.
A Simple Method for Air Volume Change Measurement in Triaxial Tests
Authors: Laudahn A , Sosna K , Boháč J
Published: March 2005

The paper presents a simple and inexpensive device to measure the volume change of the pore-air of dry soil specimens in the drained triaxial tests under atmospheric conditions. The principle of the method was described by Bishop and Henkel (Bishop and Henkel 1962). The modified apparatus makes use of low-cost photoelectric sensors and computer control. The applicability of the method is demonstrated by a comparison with test data from conventional triaxial tests on water saturated specimens.
Small-Scale Modeling of Metal-Plate-Connected Wood Truss Joints
Authors: Gupta R , Miller TH , Kittel MR
Published: March 2005

The objective of this research was to develop 1/3-scale models of full-size (prototype) metal-plate-connected wood truss joints and a complete truss using similitude theory. To verify material properties, we compared moduli of elasticity of prototype and 1/3-scale model boards. Although the variation in stiffness of the model was greater than that of the prototype, the average properties of the model and prototype were similar. The resulting average design stiffness of 1/3-scale tension splice joints was within 1 % of the prototype joint stiffness, while the ultimate load was 7 % lower than the prototype. Stiffness and strength of model heel joints were within 22 % and 17 %, respectively, of the stiffness and strength of their prototypes. Finally, ten complete model trusses were fabricated and tested; their average stiffness and strength were 780 N/mm and 17.3 kN, respectively, after scaling up by similitude. Modeling full-size truss connection behavior up to the design load, and possibly to failure, with small-scale models and similitude theory may be feasible.
Estimation of the Uncertainty of Fe in Metallic Silicon Determined by Inductively Coupled Plasmas-Atomic Emission Spectroscopy
Authors: Wang DW , Wang SW , Zhao SQ
Published: March 2005

This practice provides information for combining standard uncertainties of Fe in metallic silicon determined by the ICP-AES method of the China Inspection and Quarantine (CIQ). The measurand Fe% is determined from other quantities p.q.r. . . through a functional relationship of the model f: Fe% = f(p.q.r . . .). The estimated standard deviation associated with the output estimate Fe%, called combined standard uncertainty and denoted by uc (Fe%), is determined from the estimated standard deviation associated with each larger input estimate (p.q.r . . .). The combined variance u2c (Fe%) can be viewed, by the sensitivity coefficients, as a sum of terms with the minor errors omitted.
Evaluation of Alternative Erosion Test Methods
Authors: Meged Y
Published: March 2005

The resistance of materials to liquid impingement erosion and to cavitation erosion are considered related properties. Hence, test methods dealing with these erosion mechanisms that are covered by ASTM standards are considered as alternative tests for some applications.These methods consist of vibratory cavitation erosion, cavitating liquid jet erosion, and liquid impingement erosion.

Meaningful comparison between test results obtained by these test methods depends on a high degree of repeatability and reproducibility within each test method. These prerequisites are not met in the prevailing standards, hence it is very difficult to convert test results between them.

Increasing repeatability and reproducibility within each test method are possible. This requires the preparation of the unified specimens in a controlled way, and the application of relevant comparison criteria.
Theoretical Derivation and Experimental Examination of the Stromeyer Relation for the Analysis of Fatigue Data
Authors: Graefe W
Published: March 2005

In 1914 Stromeyer published the empirical relation ±Sn =Fl + C(106/n)1/4 for the mathematical description of fatigue (±Sn -nominal fatigue stress; Fl - fatigue limit; C - constant; n - number of stress cycles). In a previous publication Graefe has given a theoretical explanation of such a relation. In this paper the statistical distribution of the experimental fatigue data for steel is tested and no deviation from a normal distribution is found. The frequency dependence of the fatigue data is analyzed and is explained by temperature variations due to internal friction.

Different models for defect growth are in concordance with the above-mentioned formulas.
Influence of Two Hexavalent Chromium-Free Coating types on Mechanical Behavior of Bolted Joints
Authors: Nascimento H , Santos SC , Sales WF , Palma ES
Published: March 2005

The goal of this work is to evaluate the performance of two different coating technologies for bolts. They are based on zinc and aluminum with no hexavalent chromium in their composition. These technologies were implemented because international laws for environmental and human health protection are limiting the use of the hexavalent form of chromium because it causes different cancer types in workers, mainly in recycling processes. The experimental tests were performed using M12x1.25–10.9 bolts that were submitted to the test of torsion-tension. The clamping load, total torque, torque on thread, torque on the bolt head, and twist angle were measured. The friction coefficients between the nut and bolt threads, between the face of the nut and its bearing surface, the global coefficients of friction, and the nut factor were also measured and analyzed.
The Functional Requirements for Water Resistive Barriers Exposed to Incidental Water Leakage. Part 1: Classification of Membranes
Authors: Baker F , Bomberg M
Published: March 2005

This article presents a classification system for Water Resistive Barrier (WRB) products currently available on the North American market.
The Functional Requirements for Water Resistive Barriers Exposed to Incidental Water Leakage, Part 2: Testing Materials
Authors: Bomberg M , Pazera M , Onysko D
Published: March 2005

The first part of this paper presented classification of Water Resistive Barrier (WRB) products.4 The main purpose of the research reported in this part is not to determine how different WRB products perform under exposure in real assemblies but to evaluate the effectiveness of the existing test methods to characterize moisture performance of WRB products. An additional purpose is to assess what properties should be determined to enable characterization of WRB for use in computer models for heat, air, and moisture (HAM) transport.

The investigation determined that the existing test methods do not provide adequate information. Therefore, new methods are proposed with a view to providing a better basis for evaluating WRB performance in wall assemblies.
A Model for Mixed-Mode Fatigue
Authors: Tamilselvan T , Lo KW , Gong YB , Zhao MM
Published: March 2005

The initial use of fracture mechanics to characterize crack growth by fatigue was by Paris. Since then, the application of fracture mechanics to fatigue problems has become routine. In the case of fatigue under mode I loading, the method of analysis, under conditions of constant amplitude and small-scale yielding, is well established. However, apart from the conditions of variable amplitude loading, large scale yielding, and short existing cracks, the procedures for analyzing fatigue under mode II and mixed-mode loading still have not been resolved. A general model, applicable to pure and mixed-mode fatigue crack growth, has been developed based on the unified model. The formulation of the general model is in terms of a power law relationship that is an extension of Paris. The experimental procedures for the measurement of mode II and mixed-mode fatigue crack growth, and verification of the proposed fatigue model, are dealt with herein. The verification has been confined to conditions of constant amplitude and small-scale yielding.
Numerical Investigation of Joint Effect on Shock Wave Propagation in Jointed Rock Masses
Authors: Jiao YY , Fan SC , Zhao J
Published: March 2005

To investigate the joint effect on shock wave propagation and attenuation in jointed rock masses, a small-scale field explosion test is analyzed numerically by using the three-dimensional discrete element method (3D DEM) and the three-dimensional finite difference method (3D FDM). Results show that rock joints act as a kind of filter through which only low frequency shock waves are allowed to pass. This indicates that high frequency shock waves do no harm to far-field structures when they have to travel across joint sets with specific spacing. Results also reveal that the orientation of the joint sets can remarkably affect the amplitude and frequency composition of shock waves. Furthermore, as a discontinuous numerical method, 3D DEM can capture the main features of shock waves, and most importantly, it can simulate the 3D effect of rock joints. It can be concluded that in modelling 3D shock wave propagation and attenuation in jointed rock masses, 3D DEM has unique advantages over 2D modeling, 3D FDM, and even field testing.
Experimental Designs for Reliable Detection of Linkage Disequilibrium in Unstructured Random Population Association Studies
Authors: Ball Roderick D
Published: March 2005

A method is given for design of experiments to detect associations (linkage disequilibrium) in a random population between a marker and a quantitative trait locus (QTL), or gene, with a given strength of evidence, as defined by the Bayes factor. Using a version of the Bayes factor that can be linked to the value of an F-statistic with an existing deterministic power calculation makes it possible to rapidly evaluate a comprehensive range of scenarios, demonstrating the feasibility, or otherwise, of detecting genes of small effect. The Bayes factor is advocated for use in determining optimal strategies for selecting candidate genes for further testing or applications. The prospects for fine-scale mapping of QTL are reevaluated in this framework. We show that large sample sizes are needed to detect small-effect genes with a respectable-sized Bayes factor, and to have good power to detect a QTL allele at low frequency it is necessary to have a marker with similar allele frequency near the gene.
The Origin of Subfunctions and Modular Gene Regulation
Authors: Force Allan , Cresko William A , Pickett F Bryan , Proulx Steven R , Amemiya Chris , Lynch Michael
Published: March 2005

Evolutionary explanations for the origin of modularity in genetic and developmental pathways generally assume that modularity confers a selective advantage. However, our results suggest that even in the absence of any direct selective advantage, genotypic modularity may increase through the formation of new subfunctions under near-neutral processes. Two subfunctions may be formed from a single ancestral subfunction by the process of fission. Subfunction fission occurs when multiple functions under unified genetic control become subdivided into more restricted functions under independent genetic control. Provided that population size is sufficiently small, random genetic drift and mutation can conspire to produce changes in the number of subfunctions in the genome of a species without necessarily altering the phenotype. Extensive genotypic modularity may then accrue in a near-neutral fashion in permissive population-genetic environments, potentially opening novel pathways to morphological evolution. Many aspects of gene complexity in multicellular eukaryotes may have arisen passively as population size reductions accompanied increases in organism size, with the adaptive exploitation of such complexity occurring secondarily.
Mutations of a Redundant α-Tubulin Gene Affect Caenorhabditis elegans Early Embryonic Cleavage via MEI-1/Katanin-Dependent and -Independent Pathways
Authors: Lu Chenggang , Mains Paul E
Published: March 2005

The C. elegans zygote supports both meiosis and mitosis within a common cytoplasm. The meiotic spindle is small and is located anteriorly, whereas the first mitotic spindle fills the zygote. The C. elegans microtubule-severing complex, katanin, is encoded by the mei-1 and mei-2 genes and is solely required for oocyte meiotic spindle formation; ectopic mitotic katanin activity disrupts mitotic spindles. Here we characterize two mutations that rescue the lethality caused by ectopic MEI-1/MEI-2. Both mutations are gain-of-function alleles of tba-2 α-tubulin. These tba-2 alleles do not prevent MEI-1/MEI-2 microtubule localization but do interfere with its activity. TBA-1 and TBA-2 are redundant for viability, but when katanin activity is limiting, TBA-2 is preferred over TBA-1 by katanin. This is similar to what we previously reported for the β-tubulins. Removing both preferred α- and β-isoforms results in normal development, suggesting that the katanin isoform preferences are not absolute. We conclude that while the C. elegans embryo expresses redundant α- and β-tubulin isoforms, they nevertheless have subtle functional specializations. Finally, we identified a dominant tba-2 allele that disrupts both meiotic and mitotic spindle formation independently of MEI-1/MEI-2 activity. Genetic studies suggest that this tba-2 mutation has a “poisonous” effect on microtubule function.
Using Pool Noodles to Teach Mitosis and Meiosis
Authors: Locke John , McDermid Heather E
Published: March 2005

Although mitosis and meiosis are fundamental to understanding genetics, students often find them difficult to learn. We suggest using common “pool noodles” as teaching aids to represent chromatids in classroom demonstrations. Students use these noodles to demonstrate the processes of synapsis, segregation, and recombination. Student feedback has been overwhelmingly positive.
The Ku Protein Complex Is Involved in Length Regulation of Drosophila Telomeres
Authors: Melnikova Larisa , Biessmann Harald , Georgiev Pavel
Published: March 2005

Chromosome ends in Drosophila melanogaster can be elongated either by terminal attachment of the telomere-specific retrotransposons HeT-A and TART or by terminal gene conversion. Here we show that a decrease in Ku70 or Ku80 gene dosage causes a sharp increase in the frequency of HeT-A and TART attachments to a broken chromosome end and in terminal DNA elongation by gene conversion. Loss of Ku80 has more pronounced effects than loss of Ku70. However, lower Ku70 concentration reduces the stability of terminally deficient chromosomes. Our results suggest a role of the end-binding Ku complex in the accessibility and length regulation of Drosophila telomeres.
Natural Allelic Variation in the Temperature-Compensation Mechanisms of the Arabidopsis thaliana Circadian ClockSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY685131 and AY685132.
Authors: Edwards Kieron D , Lynn James R , Gyula Péter , Nagy Ferenc , Millar Andrew J
Published: March 2005

Temperature compensation is a defining feature of circadian oscillators, yet no components contributing to the phenomenon have been identified in plants. We tested 27 accessions of Arabidopsis thaliana for circadian leaf movement at a range of constant temperatures. The accessions showed varying patterns of temperature compensation, but no clear associations to the geographic origin of the accessions could be made. Quantitative trait loci (QTL) were mapped for period and amplitude of leaf movement in the Columbia by Landsberg erecta (CoL) and Cape Verde Islands by Landsberg erecta (CvL) recombinant inbred lines (RILs) at 12°, 22°, and 27°. Six CvL and three CoL QTL were located for circadian period. All of the period QTL were temperature specific, suggesting that they may be involved in temperature compensation. The flowering-time gene GIGANTEA and F-box protein ZEITLUPE were identified as strong candidates for two of the QTL on the basis of mapping in near isogenic lines (NILs) and sequence comparison. The identity of these and other candidates suggests that temperature compensation is not wholly determined by the intrinsic properties of the central clock proteins in Arabidopsis, but rather by other genes that act in trans to alter the regulation of these core proteins.
Self-Fertilization and the Evolution of Recombination
Authors: Roze Denis , Lenormand Thomas
Published: March 2005

In this article, we study the effect of self-fertilization on the evolution of a modifier allele that alters the recombination rate between two selected loci. We consider two different life cycles: under gametophytic selfing, a given proportion of fertilizations involves gametes produced by the same haploid individual, while under sporophytic selfing, a proportion of fertilizations involves gametes produced by the same diploid individual. Under both life cycles, we derive approximations for the change in frequency of the recombination modifier when selection is weak relative to recombination, so that the population reaches a state of quasi-linkage equilibrium. We find that gametophytic selfing increases the range of epistasis under which increased recombination is favored; however, this effect is substantial only for high selfing rates. Moreover, gametophytic selfing affects the relative influence of different components of epistasis (additive × additive, additive × dominance, dominance × dominance) on the evolution of the modifier. Sporophytic selfing has much stronger effects: even a small selfing rate greatly increases the parameter range under which recombination is favored, when there is negative dominance × dominance epistasis. This effect is due to the fact that selfing generates a correlation in homozygosity at linked loci, which is reduced by recombination.
Intron Size and Exon Evolution in Drosophila
Authors: Marais Gabriel , Nouvellet Pierre , Keightley Peter D , Charlesworth Brian
Published: March 2005

We have found a negative correlation between evolutionary rate at the protein level (as measured by dN) and intron size in Drosophila. Although such a relation is expected if introns reduce Hill-Robertson interference within genes, it seems more likely to be explained by the higher abundance of cis-regulatory elements in introns (especially first introns) in genes under strong selective constraints.
Saccharomyces cerevisiae Histone H2A Ser122 Facilitates DNA Repair
Authors: Harvey Anne C , Jackson Stephen P , Downs Jessica A
Published: March 2005

DNA repair takes place in the context of chromatin. Recently, it has become apparent that proteins that make up and modulate chromatin structure are involved in the detection and repair of DNA lesions. We previously demonstrated that Ser129 in the carboxyl-terminal tail of yeast histone H2A is important for double-strand-break responses. By undertaking a systematic site-directed mutagenesis approach, we identified another histone H2A serine residue (Ser122) that is important for survival in the presence of DNA-damaging agents. We show that mutation of this residue does not affect DNA damage-dependent Rad53 phosphorylation or G2/M checkpoint responses. Interestingly, we find that yeast lacking H2A S122 are defective in their ability to sporulate. Finally, we demonstrate that H2A S122 provides a function distinct from that of H2A S129. These data demonstrate a role for H2A S122 in facilitating survival in the presence of DNA damage and suggest a potential role in mediating homologous recombination. The distinct roles of H2A S122 and S129 in mediating these responses suggest that chromatin components can provide specialized functions for distinct DNA repair and survival mechanisms and point toward the possibility of a complex DNA damage responsive histone code.
Quantitative Trait Locus Study Design From an Information Perspective
Authors: Sen Śaunak , Satagopan Jaya M , Churchill Gary A
Published: March 2005

We examine the efficiency of different genotyping and phenotyping strategies in inbred line crosses from an information perspective. This provides a mathematical framework for the statistical aspects of QTL experimental design, while guiding our intuition. Our central result is a simple formula that quantifies the fraction of missing information of any genotyping strategy in a backcross. It includes the special case of selectively genotyping only the phenotypic extreme individuals. The formula is a function of the square of the phenotype and the uncertainty in our knowledge of the genotypes at a locus. This result is used to answer a variety of questions. First, we examine the cost-information trade-off varying the density of markers and the proportion of extreme phenotypic individuals genotyped. Then we evaluate the information content of selective phenotyping designs and the impact of measurement error in phenotyping. A simple formula quantifies the information content of any combined phenotyping and genotyping design. We extend our results to cover multigenotype crosses, such as the F2 intercross, and multiple QTL models. We find that when the QTL effect is small, any contrast in a multigenotype cross benefits from selective genotyping in the same manner as in a backcross. The benefit remains in the presence of a second unlinked QTL with small effect (explaining <20% of the variance), but diminishes if the second QTL has a large effect. Software for performing power calculations for backcross and F2 intercross incorporating selective genotyping and marker spacing is available from http://www.biostat.ucsf.edu/sen.
A Gene(s) for All-trans-Retinoic Acid-Induced Forelimb Defects Mapped and Confirmed to Murine Chromosome 11
Authors: Lee Grace S , Cantor Rita M , Abnoosian Arin , Park Euisun , Yamamoto Mitsuko L , Hovland David N , Collins Michael D
Published: March 2005

All-trans-retinoic acid (RA) induces various anatomical limb dysmorphologies in mice dependent on the time of exposure. During early limb development, RA induces forelimb ectrodactyly (digital absence) with varying susceptibilities for different inbred mouse strains; C57BL/6N are highly susceptible while SWV are resistant. To isolate the genetic basis of this defect, a full-genome scan was performed in 406 backcross fetuses of F1 males to C57BL/6N females. Fetuses were exposed via a maternal injection of 75 mg of RA per kilogram of body weight on gestational day 9.25. The genome-wide analysis revealed significant linkage to a chromosome 11 locus near D11Mit39 with a maximum LOD score of 9.0 and to a chromosome 4 locus near D4Mit170. An epistatic interaction was detected between loci on chromosome 11 (D11Mit39) and chromosome 18 (D18Mit64). Linkage to the chromosome 11 locus (D11Mit39) was confirmed in RA-treated backcross fetuses of F1 females to C57BL/6N males. Loci associated with bone density/mass in both human and mouse were previously detected in the same region, suggesting a mechanistic linkage with bone homeostasis. The human syntenic region of this locus has been previously linked to Meckel syndrome; the phenotype includes postaxial polydactyly, an ectopic digital defect hypothesized to be induced by a common molecular pathway with ectrodactyly.
Transmission Ratio Distortion in Intraspecific Hybrids of Mimulus guttatus
Authors: Hall Megan C , Willis John H
Published: March 2005

We constructed a genetic linkage map between two divergent populations of Mimulus guttatus. We genotyped an F2 mapping population (N = 539) at 154 AFLP, microsatellite, and gene-based markers. A framework map was constructed consisting of 112 marker loci on 14 linkage groups with a total map length of 1518 cM Kosambi. Nearly half of all markers (48%) exhibited significant transmission ratio distortion (α = 0.05). By using a Bayesian multipoint mapping method and visual inspection of significantly distorted markers, we detected 12 transmission ratio distorting loci (TRDL) throughout the genome. The high degree of segregation distortion detected in this intraspecific map indicates substantial genomic divergence that perhaps suggests genomic incompatibilities between these two populations. We compare the pattern of transmission ratio distortion in this map to an interspecific map constructed between M. guttatus and M. nasutus. A similar level of segregation distortion is detected in both maps. Collinear regions between maps are compared to determine if there are shared genetic patterns of non-Mendelian segregation distortion within and among Mimulus species.
Characterization of Active R2 Retrotransposition in the rDNA Locus of Drosophila simulans
Authors: Zhang Xian , Eickbush Thomas H
Published: March 2005

The rRNA gene (rDNA) loci of all arthropod lineages contain non-LTR retrotransposable elements that have evolved to specifically insert into the 28S rRNA genes. Extensive in vitro experiments have been conducted to investigate the mechanism of R2 retrotransposition but little is known of the insertion frequency or cellular factors that might regulate R2 activity. In this article, isofemale lines obtained from a population of Drosophila simulans were surveyed for recent R2 insertions. Within most lines, all individuals showed the same collection of R2 insertions, providing no evidence for recent R2 activity. However, in a few of the isofemale lines, virtually all individuals differed in their R2 insertion profiles. The descendants of individual pairs of flies from these “active lines” rapidly accumulated new insertions. The frequent insertion of new R2 elements was associated with the elimination of old R2 elements from the rDNA locus. The existence of lines in which R2 retrotransposes frequently and lines in which the elements appear dormant suggests that cellular mechanisms that can regulate the activity of R2 exist. Retrotransposition activity was correlated with the number of full-length R2 elements but not with the size of the rDNA locus or the number of uninserted units.
The Structure and Population Genetics of the Breakpoints Associated With the Cosmopolitan Chromosomal Inversion In(3R)Payne in Drosophila melanogaster
Authors: Matzkin Luciano M , Merritt Thomas J S , Zhu Chen-Tseh , Eanes Walter F
Published: March 2005

We report here the breakpoint structure and sequences of the Drosophila melanogaster cosmopolitan chromosomal inversion In(3R)P. Combining in situ hybridization to polytene chromosomes and long-range PCR, we have identified and sequenced the distal and proximal breakpoints. The breakpoints are not simple cut-and-paste structures; gene fragments and small duplications of DNA are associated with both breaks. The distal breakpoint breaks the tolkin (tok) gene and the proximal breakpoint breaks CG31279 and the tolloid (tld) gene. Functional copies of all three genes are found at the opposite breakpoints. We sequenced a representative sample of standard (St) and In(3R)P karyotypes for a 2-kb portion of the tok gene, as well as the same 2 kb from the pseudogene tok fragment found at the distal breakpoint of In(3R)P chromosomes. The tok gene in St arrangements possesses levels of polymorphism typical of D. melanogaster genes. The functional tok gene associated with In(3R)P shows little polymorphism. Numerous single-base changes, as well as deletions and duplications, are associated with the truncated copy of tok. The overall pattern of polymorphism is consistent with a recent origin of In(3R)P, on the order of Ne generations. The identification of these breakpoint sequences permits a simple PCR-based screen for In(3R)P.
Bayesian Shrinkage Estimation of Quantitative Trait Loci Parameters
Authors: Wang Hui , Zhang Yuan-Ming , Li Xinmin , Masinde Godfred L , Mohan Subburaman , Baylink David J , Xu Shizhong
Published: March 2005

Mapping multiple QTL is a typical problem of variable selection in an oversaturated model because the potential number of QTL can be substantially larger than the sample size. Currently, model selection is still the most effective approach to mapping multiple QTL, although further research is needed. An alternative approach to analyzing an oversaturated model is the shrinkage estimation in which all candidate variables are included in the model but their estimated effects are forced to shrink toward zero. In contrast to the usual shrinkage estimation where all model effects are shrunk by the same factor, we develop a Bayesian method that allows the shrinkage factor to vary across different effects. The new shrinkage method forces marker intervals that contain no QTL to have estimated effects close to zero whereas intervals containing notable QTL have estimated effects subject to virtually no shrinkage. We demonstrate the method using both simulated and real data for QTL mapping. A simulation experiment with 500 backcross (BC) individuals showed that the method can localize closely linked QTL and QTL with effects as small as 1% of the phenotypic variance of the trait. The method was also used to map QTL responsible for wound healing in a family of a (MRL/MPJ × SJL/J) cross with 633 F2 mice derived from two inbred lines.
Genetical Genomics Analysis of a Yeast Segregant Population for Transcription Network Inference
Authors: Bing Nan , Hoeschele Ina
Published: March 2005

Genetic analysis of gene expression in a segregating population, which is expression profiled and genotyped at DNA markers throughout the genome, can reveal regulatory networks of polymorphic genes. We propose an analysis strategy with several steps: (1) genome-wide QTL analysis of all expression profiles to identify eQTL confidence regions, followed by fine mapping of identified eQTL; (2) identification of regulatory candidate genes in each eQTL region; (3) correlation analysis of the expression profiles of the candidates in any eQTL region with the gene affected by the eQTL to reduce the number of candidates; (4) drawing directional links from retained regulatory candidate genes to genes affected by the eQTL and joining links to form networks; and (5) statistical validation and refinement of the inferred network structure. Here, we apply an initial implementation of this strategy to a segregating yeast population. In 65, 7, and 28% of the identified eQTL regions, a single candidate regulatory gene, no gene, or more than one gene was retained in step 3, respectively. Overall, 768 putative regulatory links were retained, 331 of which are the strongest candidate links, as they were retained in the expression correlation analysis and were located within or near an eQTL subregion identified by a multimarker analysis separating multiple linked QTL. One or several biological processes were statistically significantly overrepresented in independent network structures or in highly interconnected subnetworks. Most of the transcription factors found in the inferred network had a putative regulatory link to only one other gene or exhibited cis-regulation.
Stress tolerance responses of two cotton cultivars exposed to ultraviolet-A (366 nm) radiation: photosynthetic performance and chemical constituents
Authors: Ebrahim M. K. H.
Published: March 2005

The stress tolerance responses of two Egyptian cotton cultivars (Giza 45 and 86) exposed to various doses (40, 80, 160 and 320 min) of artificial ultraviolet-A (366 nm) radiation were investigated. The seed germination of Giza 86 was promoted at 40 min, but substantially inhibited at 80 and 160 min and completely suppressed at 320 min. However, the seed germination of Giza 45 was progressively inhibited by UV-A exposure and ceased at 160 min, so doses of 40 and 80 min were selected for further studies. In contrast to seed germination, the seedling growth of Giza 86 was negatively affected at 40 min. UV-A stress induced a great reduction in the leaf carbohydrates as well as in the viability and dry mass production of the shoots of both cultivars, but the response was comparatively higher in Giza 45. It also decreased the chorophyll (Chl) and carotenoid contents, coupled with an increase in the Chla/bratio, diminished the Hill reaction activity, and quenched the Chlafluorescence both in the presence and absence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea, suggesting an inhibitory effect on the water-splitting system (donor side) as well as on the electron transport from the primary to the secondary acceptors of PSII (acceptor side). These changes reflect a disturbance in the structure, composition and function of the photosynthetic apparatus as well as the sensitivity of PSII to UV-A stress. Nucleic acids (DNA and RNA) were markedly damaged by exposure to UV-A for 80 min, while both cultivars developed adaptive mechanisms for damage moderation. These mechanisms involved increasing the levels of flavonoids, total lipids and total soluble proteins as well as having smaller, thicker leaf blades. Since Giza 86 showed a comparatively higher level of adaptation, it tolerates UV-A stress better than Giza 45.Abbreviations:Car, carotenoids; Chl, chlorophyll; DCMU, 3-(3,4-dichlorophenyl)-1,1-dimethylurea; DCPIP, 2,6-dichlorophenol indophenol; DNA, deoxyribonucleic acid; d.m., dry mass; f.m., fresh mass; PSII, photosystem II; RNA, ribonucleic acid; TSP, total soluble proteins; UV-AR, ultraviolet-A (366 nm) radiation.
Effect of herbicides on the weed infestation and grain yield of soybean (Glycine max)
Authors: Singh G. , Jolly R. S.
Published: March 2005

Two field experiments were conducted during the kharif (rainy) season of 1999 and 2000 on a loamy sand soil to study the effect of various pre- and post-emergence herbicides on the weed infestation and grain yield of soybean. The presence of weeds in the weedy control plots resulted in 58.8 and 58.1% reduction in the grain yield in the two years compared to two hand weedings (HW) at 30 and 45 days after sowing (DAS), which gave grain yields of 1326 and 2029 kg ha-1. None of the herbicides was significantly superior to the two hand weedings treatment in influencing the grain yield. However, the pre-emergence application of 0.75 kg ha-1 S-metolachlor, and 0.5 kg ha-1 pendimethalin (pre-emergence) + HW 30 DAS were at par or numerically superior to this treatment. There was a good negative correlation between the weed dry matter at harvest and the grain yield of soybean, which showed that effective weed control is necessary for obtaining higher yields of soybean.
Concentration and uptake of secondary nutrients (Ca, Mg, S) in rice as influenced by duration of variety and nitrogen fertilization
Authors: Lakshmanan R. , Prasad R.
Published: March 2005

A field experiment was conducted for 2 years at the Indian Agricultural Research Institute, New Delhi to study the effects of duration of variety and nitrogen fertilization on the Ca, Mg and S concentration and uptake in rice. In general, the concentrations of Ca, Mg and S were not significantly influenced by the duration of the rice variety. N fertilization had a tendency to increase the concentration of Ca, Mg and S at 45 days after transplanting as well as at harvest; however, the difference was significant only in the case of the Ca concentration in the grain and only when the N level was raised from 60 to 120 kg N/ha. The duration of the rice variety had a significant effect on the Ca, Mg and S uptake by the straw and grain at harvest, which was higher in the medium duration variety Pusa Basmati-1 than in Pusa Jaldi Dhan-1, mainly due to the higher yields obtained with the former cultivar. Nitrogen application significantly increased the Ca, Mg and S uptake at harvest mainly due to its increasing effects on the grain and straw yields of rice. The average uptake of Ca, Mg and S was 12.6, 13.6 and 3.5 kg per metric ton of grain, respectively.
Interaction of saline water and nitrogen on the partitioning and statistical correlation of mineral elements in maize plants
Authors: Irshad M. , Honna T. , Yamamoto S. , KAto M. ,   et al.
Published: March 2005

Saline irrigation water has a tremendous impact on the yield potential of crops. The distribution of mineral elements and their ratios in maize plant organs in response to saline water and nitrogen (N) nutrition was studied in a pot experiment for six weeks. The plants were separated into leaf, stalk and root and analysed for calcium (Ca), magnesium (Mg), sodium (Na), potassium (K) and chloride (Cl) contents. The partitioning and ratios of mineral nutrients in plants were significantly affected by water salinity and nitrogen level. In saline water the roots contained the highest Na content; Ca and Mg were higher in the leaf, whereas K and Cl were highest in the stalk. In non-saline water, Na and Cl were highest in the root and the remaining elements were greatest in the stalk. The K and Cl contents were significantly reduced by an increase in the N level, whereas the reverse was true for the Ca, Mg and Na contents. An inverse relationship was noted for the plant biomass versus both Na uptake and the Na/Ca, Na/Mg and Na/K ratios in plants irrigated with saline water. The mineral elements, with the exception of K, appeared to be highly correlated in the plant parts.
Responses of soybean genotypes to intercropping with maize in the Southern Guinea Savanna, Nigeria
Authors: Egbo C. U. , Adagba M. A. , Adedzwa D. K.
Published: March 2005

Field trials were conducted in the wet seasons of 1997 and 1998 at Makurdi, Otukpo and Yandev in the Southern Guinea Savanna ecological zone of Nigeria to study the responses of ten soybean genotypes to intercropping. The experiment was laid out in a randomised complete block design. The genotypes TGX 1807-19F, NCRI-Soy2, Cameroon Late and TGX 1485-1D had the highest grain yield. All the Land Equivalent Ratio (LER) values were higher than unity, indicating that there is great advantage in intercropping maize with soybean. The yield of soybean was positively correlated with the days to 50% flowering, days to maturity, plant height, pods/plant and leaf area, indicating that an improvement in any of these traits will be reflected in an increase in seed yield. There was a significant genotype × yield × location interaction for all traits. This suggests that none of these factors acted independently. Similarly, the genotype × location interaction was more important than the genotype × year interaction for seed yield, indicating that the yield response of the ten soybean genotypes varied across locations rather than across years. Therefore, using more testing sites for evaluation may be more important than the number of years.