bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinguishing Between Selective Sweeps and Demography Using DNA Polymorphism Data
Authors: Jensen Jeffrey D , Kim Yuseob , DuMont Vanessa Bauer , Aquadro Charles F , Bustamante Carlos D 
Published: May 2005

Abstract
In 2002 Kim and Stephan proposed a promising composite-likelihood method for localizing and estimating the fitness advantage of a recently fixed beneficial mutation. Here, we demonstrate that their composite-likelihood-ratio (CLR) test comparing selective and neutral hypotheses is not robust to undetected population structure or a recent bottleneck, with some parameter combinations resulting in a false positive rate of nearly 90%. We also propose a goodness-of-fit test for discriminating rejections due to directional selection (true positive) from those due to population and demographic forces (false positives) and demonstrate that the new method has high sensitivity to differentiate the two classes of rejections.
The Rate of Compensatory Mutation in the DNA Bacteriophage φX174
Authors: Poon Art , Chao Lin 
Published: May 2005

AbstractA compensatory mutation occurs when the fitness loss caused by one mutation is remedied by its epistatic interaction with a second mutation at a different site in the genome. This poorly understood biological phenomenon has important implications, not only for the evolutionary consequences of mutation, but also for the genetic complexity of adaptation. We have carried out the first direct experimental measurement of the average rate of compensatory mutation. An arbitrary selection of 21 missense substitutions with deleterious effects on fitness was introduced by site-directed mutagenesis into the bacteriophage φX174. For each deleterious mutation, we evolved 8–16 replicate populations to determine the frequency at which a compensatory mutation, instead of the back mutation, was acquired to recover fitness. The overall frequency of compensatory mutation was ∼70%. Deleterious mutations that were more severe were significantly more likely to be compensated for. Furthermore, experimental reversion of deleterious mutations revealed that compensatory mutations have deleterious effects in a wild-type background. A large diversity of intragenic compensatory mutations was identified from sequencing fitness-recovering genotypes. Subsequent analyses of intragenic mutation diversity revealed a significant degree of clustering around the deleterious mutation in the linear sequence and also within folded protein structures. Moreover, a likelihood analysis of mutation diversity predicts that, on average, a deleterious mutation can be compensated by about nine different intragenic compensatory mutations. We estimate that about half of all compensatory mutations are located extragenically in this organism.
In Vivo Characterization of the Nonessential Budding Yeast Anaphase-Promoting Complex/Cyclosome Components Swm1p, Mnd2p and Apc9p
Authors: Page Andrew M , Aneliunas Vicky , Lamb John R , Hieter Philip 
Published: May 2005

AbstractWe have examined the in vivo requirement of two recently identified nonessential components of the budding yeast anaphase-promoting complex, Swm1p and Mnd2p, as well as that of the previously identified subunit Apc9p. swm1Δ mutants exhibit synthetic lethality or conditional synthetic lethality with other APC/C subunits and regulators, whereas mnd2Δ mutants are less sensitive to perturbation of the APC/C. swm1Δ mutants, but not mnd2Δ mutants, exhibit defects in APC/C substrate turnover, both during the mitotic cell cycle and in α-factor-arrested cells. In contrast, apc9Δ mutants exhibit only minor defects in substrate degradation in α-factor-arrested cells. In cycling cells, degradation of Clb2p, but not Pds1p or Clb5p, is delayed in apc9Δ. Our findings suggest that Swm1p is required for full catalytic activity of the APC/C, whereas the requirement of Mnd2p for APC/C function appears to be negligible under standard laboratory conditions. Furthermore, the role of Apc9p in APC/C-dependent ubiquitination may be limited to the proteolysis of a select number of substrates.
Bayesian Model Selection for Genome-Wide Epistatic Quantitative Trait Loci Analysis
Authors: Yi Nengjun , Yandell Brian S , Churchill Gary A , Allison David B , Eisen Eugene J , Pomp Daniel 
Published: May 2005

Abstract
The problem of identifying complex epistatic quantitative trait loci (QTL) across the entire genome continues to be a formidable challenge for geneticists. The complexity of genome-wide epistatic analysis results mainly from the number of QTL being unknown and the number of possible epistatic effects being huge. In this article, we use a composite model space approach to develop a Bayesian model selection framework for identifying epistatic QTL for complex traits in experimental crosses from two inbred lines. By placing a liberal constraint on the upper bound of the number of detectable QTL we restrict attention to models of fixed dimension, greatly simplifying calculations. Indicators specify which main and epistatic effects of putative QTL are included. We detail how to use prior knowledge to bound the number of detectable QTL and to specify prior distributions for indicators of genetic effects. We develop a computationally efficient Markov chain Monte Carlo (MCMC) algorithm using the Gibbs sampler and Metropolis-Hastings algorithm to explore the posterior distribution. We illustrate the proposed method by detecting new epistatic QTL for obesity in a backcross of CAST/Ei mice onto M16i.
Sobo, a Recently Amplified Satellite Repeat of Potato, and Its Implications for the Origin of Tandemly Repeated Sequences
Authors: Tek Ahmet L , Song Junqi , Macas Jiri , Jiang Jiming 
Published: May 2005

Abstract
Highly repetitive satellite DNA sequences are main components of heterochromatin in higher eukaryotic genomes. It is well known that satellite repeats can expand and contract dramatically, which may result in significant genome size variation among genetically related species. The origin of satellite repeats, however, is elusive. Here we report a satellite repeat, Sobo, from a diploid potato species, Solanum bulbocastanum. The Sobo repeat is mapped to a single location in the pericentromeric region of chromosome 7. This single Sobo locus spans ∼360 kb of a 4.7-kb monomer. Sequence analysis revealed that the major part of the Sobo monomer shares significant sequence similarity with the long terminal repeats (LTRs) of a retrotransposon. The Sobo repeat was not detected in other Solanum species and is absent in some S. bulbocastanum accessions. Sobo monomers are highly homogenized and share &gt;99% sequence identity. These results suggest that the Sobo repeat is a recently emerged satellite and possibly originated by a sudden amplification of a genomic region including the LTR of a retrotransposon and its flanking genomic sequences.
Genetic Analysis Reveals a Role for the C Terminus of the Saccharomyces cerevisiae GTPase Snu114 During Spliceosome Activation
Authors: Brenner Tamara J , Guthrie Christine 
Published: May 2005

Abstract
Snu114 is the only GTPase required for mRNA splicing. As a homolog of elongation factor G, it contains three domains (III–V) predicted to undergo a large rearrangement following GTP hydrolysis. To assess the functional importance of the domains of Snu114, we used random mutagenesis to create conditionally lethal alleles. We identified three main classes: (1) mutations that are predicted to affect GTP binding and hydrolysis, (2) mutations that are clustered in 10- to 20-amino-acid stretches in each of domains III–V, and (3) mutations that result in deletion of up to 70 amino acids from the C terminus. Representative mutations from each of these classes blocked the first step of splicing in vivo and in vitro. The growth defects caused by most alleles were synthetically exacerbated by mutations in PRP8, a U5 snRNP protein that physically interacts with Snu114, as well as in genes involved in snRNP biogenesis, including SAD1 and BRR1. The allele snu114-60, which truncates the C terminus, was synthetically lethal with factors required for activation of the spliceosome, including the DExD/H-box ATPases BRR2 and PRP28. We propose that GTP hydrolysis results in a rearrangement between Prp8 and the C terminus of Snu114 that leads to release of U1 and U4, thus activating the spliceosome for catalysis.
On curves contained in convex subsets of the plane
Authors: Coppersmith Don , Nagy Győző , Ravsky Sasha 
Published: May 2005

If K' ? K are convex bodies of the plane then the perimeter of K' is not greater than the perimeter of K. We obtain the following generalization of this fact. Let K be a convex compact body of the plane with perimeter p and diameter d and let r ? 1 be an integer. Let s be the smallest number such that for any curve of length greater than s contained in K there is a straight line intersecting the curve at least in r+1 different points. Then s = rp/2 if r is even and s = (r-1) p/2 + d if r is odd.
In Situ Hybridization to Metaphase Chromosomes and Interphase Nuclei
Authors: Knoll Joan H. M. , Lichter Peter 
Published: May 2005

AbstractIn situ hybridization is used to determine the chromosomal map location and the relative order of genes and DNA sequences within a chromosomal band. It can also be used to detect aneuploidy, gene amplification, and subtle chromosomal rearrangements. Fluorescence in situ hybridization (FISH), probably the most widely used method, is described in the first basic protocol. Two support protocols are provided to amplify weak fluorescent signals obtained in FISH. Nonisotopic probes can also be detected by enzymatic reactions using horseradish peroxidase or alkaline phosphatase, as described in alternate protocols. Nonisotopic labeling of DNA probes by nick translation is described in a support protocol. The order of closely spaced FISH probes along chromosomes in interphase nuclei can be determined. A basic protocol for isotopic in situ hybridization (IISH) with 3H is provided followed by a support protocol for preparation of autoradiographic emulsion.
Strategies for Large‐Insert Cloning and Analysis
Authors: Smith Douglas R. , Moir Donald T. 
Published: May 2005

AbstractThis revised introduction provides an up‐to‐date overview of available resources and methods for identifying, mapping, manipulating, and analyzing large‐insert (BAC, YAC, PAC, and P1) clones from the human genome or from other genomes. The table listing available libraries and clone resources has been updated, emphasizing widely used resources that are readily available and that were also used to map and sequence the human genome. Mapping references have been updated, along with links to web sites that provide online access to integrated mapping and sequencing resources. Additional information is included on restriction endonuclease fingerprinting approaches and on transformation‐associated recombination (TAR) cloning methods for rescue of genes or genomic segments from specific cell types or individuals.
An Overview of Spotfire for Gene‐Expression Studies
Authors: Kaushal Deepak , Naeve Clayton W. 
Published: May 2005

AbstractSpotfire DecisionSite for Functional Genomics (referred to here as Spotfire) is a powerful data mining and visualization application with use in many disciplines. This unit provides an overview of Spotfire's utility in analyzing gene expression data obtained from DNA microarray experiments. Analysis of microarray data requires software‐based solutions able to handle and manipulate the enormous amount of data generated. Spotfire provides a solution for accessing, analyzing and visualizing data generated from microarray experiments. Spotfire is designed to allow biologists with little or no programming or statistical skills to transform, process, and analyze microarray data.
Standardization, Calibration, and Control in Flow Cytometry
Authors: Hoffman Robert A. 
Published: May 2005

AbstractBecause flow cytometers are designed to measure particle characteristics, particles are the most common materials used to calibrate, control, and standardize the instruments. Definitions are provided for common terms to alert the reader to critical distinctions in meaning. The unit presents extensive background on particle types and cautions and goes on to describe practical aspects of methods to standardize and calibrate instruments, in terms of optical alignment, fluorescence and light scatter resolution, and sensitivity. Finally, suggestions follow for analyzing particles used for calibration.
Multiparameter Analysis of Intracellular Phosphoepitopes in Immunophenotyped Cell Populations by Flow Cytometry
Authors: Perez Omar D. , Mitchell Dennis , Campos Roberto , Gao Guo‐Jian , Li Li , Nolan Garry P. 
Published: May 2005

AbstractThis unit presents protocols for measuring intracellular phosphoepitopes by flow cytometry for biochemical investigations in both human and murine primary cells as well as in cell lines. Conventional methods that require cellular lysis cannot discriminate between proteins from different cellular subsets. Intracellular detection of phosphorylated and nonphosphorylated signaling molecules, on the other hand, has recently exposed the heterogeneity that can be observed upon signal transduction. Although staining methodologies for cytokines and cell cycle antigens have been appreciated for years, detection of phosphorylated molecules presents several new challenges, including generation of reagents and details of the staining technique. As these techniques are adapted to new applications, the protocols continue to be refined. This unit describes signal amplification of intracellular signals upon detergent‐based permeabilizations, staining protocol for adherent cells, methodology for whole‐blood staining, and multiparameter staining procedures for surface and intracellular antigens.
Output‐feedback co‐ordinated decentralized adaptive tracking: The case of MIMO subsystems with delayed interconnections
Authors: Mirkin Boris M. , Gutman Per‐Olof 
Published: May 2005

AbstractExact decentralized output‐feedback Lyapunov‐based designs of direct model reference adaptive control (MRAC) for linear interconnected delay systems with MIMO subsystems are introduced. The design process uses a co‐ordinated decentralized structure of adaptive control with reference model co‐ordination which requires an exchange of signals between the different reference models. It is shown that in the framework of the reference model co‐ordination zero residual tracking error is possible, exactly as in the case with SISO subsystems. We develop decentralized MRAC on the base ofa prioriinformation about only the local subsystems gain frequency matrices without additionala prioriknowledge about the full system gain frequency matrix. To achieve a better adaptation performance we propose proportional, integral time‐delayed adaptation laws. The appropriate Lyapunov–Krasovskii type functional is suggested to design the update mechanism for the controller parameters, and in order to prove stability. Two different adaptive DMRAC schemes are proposed, being the first asymptotic exact zero tracking results for linear interconnected delay systems with MIMO subsystems. Copyright © 2005 John Wiley & Sons, Ltd.
Block Copolymer Nanocomposites: Perspectives for Tailored Functional Materials
Authors: Bockstaller M. R. , Mickiewicz R. A. , Thomas E. L. 
Published: May 2005

AbstractHeterogeneous materials in which the characteristic length scale of the filler material is in the nanometer range—i.e., nanocomposites—is currently one of the fastest growing areas of materials research. Polymer nanocomposites have expanded beyond the original scope of polymer–nanocrystal dispersions for refractive‐index tuning or clay‐filled homopolymers primarily pursued for mechanical reinforcement, to include a wide range of applications. This article highlights recent research efforts in the field of structure formation in block copolymer‐based nanocomposite materials, and points out opportunities for novel materials based on inclusion of different types of nanoparticles. The use of block copolymers instead of homopolymers as the matrix is shown to afford opportunities for controlling the spatial and orientational distribution of the nanoelements. This, in turn, allows much more sophisticated tailoring of the overall properties of the composite material.
Electrowinning of copper in a lab‐scale squirrel‐cage cell with anion membrane
Authors: Cifuentes L. , Ortiz R. , Casas J. M. 
Published: May 2005

AbstractThis work describes the design and optimization of a laboratory‐scale copper electrowinning cell based on reactive electrodialysis that incorporates a cathode made of copper granules contained in a rotating squirrel‐cage–type enclosure. It also incorporates the Fe2+ → Fe3+ + e anodic reaction to overcome the principal disadvantages of conventional electrowinning technology. With this design, anolyte (aqueous FeSO4 + H2SO4) and catholyte (aqueous CuSO4 + H2SO4) are kept separate by an anion membrane that prevents cation transport between the electrolytes. Experiments were carried out to characterize cell performance under various conditions, and results show that energy requirements with this cell can be 25% lower than conventional industrial values. The same results also show that the squirrel‐cage cell can be used to electrowin copper from impoverished electrolytes. © 2005 American Institute of Chemical Engineers AIChE J, 2005
Cavitation in creeping shear flows
Authors: Kottke Peter A. , Bair Scott S. , Winer Ward O. 
Published: May 2005

AbstractLiquid failure has been observed in low Reynolds number (Stokes) shear flows where reduction of the hydrodynamic pressure should not occur. Cavitation in Stokes flows has implications in lubrication, polymer processing, and rheological measurements. Such cavitation can be predicted by a principal normal stress cavitation criterion (PNSCC). We present results of a direct experimental test of the PNSCC. Imaging of the cavitation events suggests that the cavitation is gaseous and originates from preexisting nuclei. Crevice‐stabilized gas nuclei are assumed, and numerical simulations are used to investigate the cavitation event for a Newtonian liquid. The inception of cavitation from a preexisting nucleus, the persistence of suitable nuclei, and the growth and deformation of shed bubbles are considered. © 2005 American Institute of Chemical Engineers AIChE J, 2005
Local liquid holdups and hysteresis in a 2‐D packed bed using X‐ray radiography
Authors: Basavaraj M. G. , Gupta G. S. , Naveen K. , Rudolph V. , Bali R. 
Published: May 2005

AbstractAn X‐ray visualization technique has been used for the quantitative determination of local liquid holdups distribution and liquid holdup hysteresis in a nonwetting two‐dimensional (2‐D) packed bed. A medical diagnostic X‐ray unit has been used to image the local holdups in a 2‐D cold model having a random packing of expanded polystyrene beads. An aqueous barium chloride solution was used as a fluid to achieve good contrast on X‐ray images. To quantify the local liquid holdup, a simple calibration technique has been developed that can be used for most of the radiological methods such as gamma ray and neutron radiography. The global value of total liquid holdup, obtained by X‐ray method, has been compared with two conventional methods: drainage and tracer response. The X‐ray technique, after validation, has been used to visualize and quantify the liquid hysteresis phenomena in a packed bed. The liquid flows in preferred paths or channels that carry droplets/rivulets of increasing size and number as the liquid flow rate is increased. When the flow is reduced, these paths are retained and the higher liquid holdup that persists in these regions leads to the holdup hysteresis effect. Holdup in some regions of the packed bed may be an order of magnitude higher than average at a particular flow rate. © 2005 American Institute of Chemical Engineers AIChE J, 2005
Gas absorption in a wetted‐wire column
Authors: Migita Hirofumi , Soga Kohei , Mori Yasuhiko H. 
Published: May 2005

AbstractThis study aims to examine the performance, as a gas absorber, of a “wetted‐wire column,” a novel gas–liquid contact device equipped with a bundle of built‐in vertically oriented wires. This device allows a liquid absorbent to flow down each wire, being in contact with a gas mixture flowing countercurrently. A prototype column having 109 wires was constructed and then tested in experimental CO2‐absorption operations, using aqueous monoethanolamine absorbents. In every operation, a monoethanolamine solution was supplied to the column at a constant rate such that its flow on each wire assumed a “string‐of‐beads” pattern consisting of annular thin liquid films sheathing the wire and teardrop‐shaped liquid beads alternately aligned on the wire at regular intervals. It was confirmed that the wetted‐wire column has an absorption performance quite comparable to conventional packed‐bed columns, while it imposes, on the internal gas flow, only a pressure loss smaller than that in packed‐bed columns of the same height by one to two orders. © 2005 American Institute of Chemical Engineers AIChE J, 2005
Gas–liquid catalytic hydrogenation reaction in small catalyst channel
Authors: Liu Wei , Roy Shantanu , Fu Xiaodong 
Published: May 2005

AbstractA study is presented on the performance potential of gas–liquid–solid multiphase catalytic reactions in small‐size structured catalyst/reactor channels. A hydrogenation reaction is performed over the Ni/alumina monolith catalyst module with a model feed consisting of styrene, 1‐octene, and toluene. The gas/liquid feed stream is directly delivered into a single, representative channel of the multichannel monolith catalyst module to eliminate any flow distribution problem. The reaction tests are conducted with different channel sizes, wall structures, and feed compositions. The cocurrent downflow operation is compared to the cocurrent upflow. The olefin hydrogenation reaction is found to be severely limited by mass‐transfer rates. Because of intensified mass transfer inside the small catalyst channel, substantial olefin conversion (>50%) is achieved even at unconventionally high LHSV (∼2000 v/v/h). Liquid and gas superficial linear velocities were varied over a wide range (UL = 1–50 cm/s, UG = 1–2000 cm/s) to elucidate effects of possibly different flow regimes on the reaction performance. The mass‐transfer rate constant of liquid reactant from bulk fluid onto the channel surface in a 1‐mm reaction channel is found to be related to the flow conditions by a simple equation, akLS (1/s) = 0.094(UL + 0.1UG)0.788. The mass‐transfer equation is useful for selection of suitable flow conditions for a given catalytic reaction rate. © 2005 American Institute of Chemical Engineers AIChE J, 2005