bluuebunny/crossref_metadata_2025 huggingface dataset:
Axonal plasticity and functional recovery after spinal cord injury in mice deficient in both glial fibrillary acidic protein and vimentin genes
Authors: Menet V. , Prieto M. , Privat A. , Ribotta M. Giménez y
Published: July 2003

The lack of axonal regeneration in the injured adult mammalian spinal cord
leads to permanent functional disabilities. The inability of neurons to
regenerate their axon is appreciably due to an inhospitable environment made
of an astrocytic scar. We generated mice knock-out for glial fibrillary acidic
protein and vimentin, the major proteins of the astrocyte cytoskeleton, which
are upregulated in reactive astrocytes. These animals, after a hemisection of
the spinal cord, presented reduced astroglial reactivity associated with
increased plastic sprouting of supraspinal axons, including the reconstruction
of circuits leading to functional restoration. Therefore, improved anatomical
and functional recovery in the absence of both proteins highlights the pivotal
role of reactive astrocytes in axonal regenerative failure in adult CNS and
could lead to new therapies of spinal cord lesions.
The neuropeptide galanin modulates behavioral and neurochemical signs of opiate withdrawal
Authors: Zachariou Venetia , Brunzell Darlene H. , Hawes Jessica , Stedman Diann R. , Bartfai Tamas , Steiner Robert A. , Wynick David , Langel Ülo , Picciotto Marina R.
Published: July 2003

Much research has focused on pathways leading to opiate addiction. Pathways opposing addiction are more difficult to study but may be critical in developing interventions to combat drug dependence and withdrawal. Galanin decreases firing of locus coeruleus neurons, an effect hypothesized to decrease signs of opiate withdrawal. The current study addresses whether galanin affects morphine withdrawal signs by using a galanin agonist, galnon, that crosses the blood–brain barrier, and mice genetically engineered to under- or overexpress galanin peptide. Galnon significantly decreased morphine withdrawal signs in C57BL/6 mice. Further, knockout mice lacking galanin showed exacerbated morphine withdrawal signs, suggesting that endogenous galanin normally counteracts opiate withdrawal. Transgenic mice overexpressing galanin in noradrenergic neurons also showed decreased morphine withdrawal signs, suggesting a possible neuroanatomical locus for these effects of galanin. Both c-fos immunoreactivity, a marker of neuronal activity, and phosphorylation of tyrosine hydroxylase at Ser-40, a marker of cAMP levels, are decreased in the locus coeruleus by galnon treatment after morphine withdrawal, suggesting a possible molecular mechanism for the behavioral effects of galanin. These studies suggest that galanin normally acts to counteract opiate withdrawal and that small molecule galanin agonists could be effective in diminishing the physical signs of withdrawal.
What drives the translocation of stiff chains?
Authors: Zandi Roya , Reguera David , Rudnick Joseph , Gelbart William M.
Published: July 2003

We study the dynamics of the passage of a stiff chain through a pore into a
cell containing particles that bind reversibly to it. Using Brownian molecular
dynamics simulations we investigate the mean first-passage time as a function
of the length of the chain inside for different concentrations of binding
particles. As a consequence of the interactions with these particles, the
chain experiences a net force along its length whose calculated value from the
simulations accounts for the velocity at which it enters the cell. This force
can in turn be obtained from the solution of a generalized diffusion equation
incorporating an effective Langmuir adsorption free energy for the chain plus
binding particles. These results suggest a role of binding particles in the
translocation process that is in general quite different from that of a
Brownian ratchet. Furthermore, nonequilibrium effects contribute significantly
to the dynamics; e.g., the chain often enters the cell faster than particle
binding can be saturated, resulting in a force several times smaller than the
equilibrium value.
In vivodynamics of antigen-specific regulatory T cells not predicted from behaviorin vitro
Authors: Klein Ludger , Khazaie Khashayarsha , von Boehmer Harald
Published: July 2003

Adoptive transfer of antigen-specific CD25+CD4+regulatory T cells was used to analyze the stability of their phenotype, their behavior after immunization, and their mode of suppressing cotransferred naive T cellsin vivo. We found that regulatory T cells maintained their phenotype in the absence of antigen, were not anergicin vivo, and proliferated as extensively as naive CD4+T cells after immunization without losing their suppressive functionin vivoandin vitro. In vivo, the expansion of cotransferred naive T cells was suppressed relatively late in the response such that regulatory T cells expressing mostly IL-10 but not IL-2 or IFN-γ represented the dominant subset of cells. Our results reveal properties of regulatory T cells that were not predicted fromin vitrostudies.
The speed of the flagellar rotary motor of
Escherichia coli
varies linearly with protonmotive force
Authors: Gabel Christopher V. , Berg Howard C.
Published: July 2003

A protonmotive force (pmf) across the cell's inner membrane powers the
flagellar rotary motor of
Escherichia coli
. Speed is known to be
proportional to pmf when viscous loads are heavy. Here we show that speed also
is proportional to pmf when viscous loads are light. Two motors on the same
bacterium were monitored as the cell was slowly deenergized. The first motor
rotated the entire cell body (a heavy load), while the second motor rotated a
small latex bead (a light load). The first motor rotated slowly and provided a
measure of the cell's pmf. The second motor rotated rapidly and was compared
with the first, to give the speed–pmf relation for light loads.
Experiments were done at 24.0°C and 16.2°C, with initial speeds
indicating operation well into the high-speed, low-torque regime. Speed was
found to be proportional to pmf over the entire (accessible) dynamic range
(0–270 Hz). If the passage of a fixed number of protons carries the
motor through each revolution, i.e., if the motor is tightly coupled, a linear
speed–pmf relation is expected close to stall, where the work done
against the viscous load matches the energy dissipated in proton flow. A
linear relation is expected at high speeds if proton translocation is
rate-limiting and involves multiple steps, a model that also applies to simple
proton channels. The present work shows that a linear relation is true more
generally, providing an additional constraint on possible motor
mechanisms.
The degradation of promyelocytic leukemia and Sp100 proteins by herpes simplex virus 1 is mediated by the ubiquitin-conjugating enzyme UbcH5a
Authors: Gu Haidong , Roizman Bernard
Published: July 2003

Infected cell protein 0 (ICP0) of herpes simplex virus 1 expresses two E3
ubiquitin (Ub) ligase activities mapping in the domains encoded by exons 2 and
3, respectively. Site 1 (exon 3) is responsible for the degradation of the E2
Ub-conjugating enzyme cdc34 whereas site 2 (exon 2) is associated with a ring
finger and has been shown to mediate the degradation of promyelocytic leukemia
(PML) and Sp100 proteins and the dispersal of nuclear domain 10 (ND10). In
in vitro
assays site 2 polyubiquitylates the E2 enzymes UbcH5a and
UbcH6 but not other (e.g., UbcH7) enzymes. In this article, we show that
ectopic expression of dominant negative UbcH5a carrying the substitution C85A
delayed or blocked the degradation of PML and Sp100 and dispersal of ND10
whereas ectopic expression of wild-type UbcH5a or dominant negative UbcH6 and
UbcH7 carrying the substitutions C131A and C86A, respectively, had no effect.
These results link the degradation of PML and Sp100 and the dispersal of ND10
to the E3 activities of ICP0 associated with the UbcH5a E2 enzyme.
Gene transfer establishes primacy of striated vs. smooth muscle sarcoglycan complex in limb-girdle muscular dystrophy
Authors: Durbeej Madeleine , Sawatzki Shanna M. , Barresi Rita , Schmainda Kathleen M. , Allamand Valérie , Michele Daniel E. , Campbell Kevin P.
Published: July 2003

Limb-girdle muscular dystrophy types 2E and F are characterized by skeletal
muscle weakness and often cardiomyopathy and are due to mutations in the genes
encoding β- and δ-sarcoglycan. We previously demonstrated that loss
of sarcoglycans in smooth muscle leads to constrictions of the
microvasculature that contributes to the cardiac phenotype. It is unclear how
vasculature abnormalities affect skeletal muscle. We injected recombinant
β- or δ-sarcoglycan adenoviruses into skeletal muscles of
corresponding null mice. We hypothesized that the adenoviruses would not
transduce vascular smooth muscle, and we would only target skeletal muscle.
Indeed, sustained expression of intact sarcoglycan–sarcospan complex was
noted at the sarcolemma, neuromuscular junction, myotendinous junction, and in
peripheral nerve, but not in vascular smooth muscle. Gene transfer of the
corresponding deleted sarcoglycan gene preserved sarcolemmal integrity,
prevented pathological dystrophy and hypertrophy, and protected against
exercised-induced damage. We conclude that vascular dysfunction is not a
primary cause of β- and δ-sarcoglycan-deficient muscular dystrophy.
In addition, we show successful functional rescue of entire muscles after
adenovirus-mediated gene delivery. Thus, virus-mediated gene transfer of
sarcoglycans to skeletal muscle in combination with pharmacological prevention
of cardiomyopathy constitute promising therapeutic strategies for limb-girdle
muscular dystrophies.
Poly(γ-d-glutamic acid) protein conjugates induce IgG antibodies in mice to the capsule ofBacillus anthracis: A potential addition to the anthrax vaccine
Authors: Schneerson Rachel , Kubler-Kielb Joanna , Liu Teh-Yung , Dai Zhong-Dong , Leppla Stephen H. , Yergey Alfred , Backlund Peter , Shiloach Joseph , Majadly Fathy , Robbins John B.
Published: July 2003

Both the protective antigen (PA) and the poly(γ-d-glutamic acid) capsule (γdPGA) are essential for the virulence ofBacillus anthracis. A critical level of vaccine-induced IgG anti-PA confers immunity to anthrax, but there is no information about the protective action of IgG anti-γdPGA. Because the number of spores presented by bioterrorists might be greater than encountered in nature, we sought to induce capsular antibodies to expand the immunity conferred by available anthrax vaccines. The nonimmunogenic γdPGA or corresponding synthetic peptides were bound to BSA, recombinantB. anthracisPA (rPA), or recombinantPseudomonas aeruginosaexotoxin A (rEPA). To identify the optimal construct, conjugates ofB. anthracisγdPGA,Bacillus pumilusγdLPGA, and peptides of varying lengths (5-, 10-, or 20-mers), of thedorlconfiguration with active groups at the N or C termini, were bound at 5–32 mol per protein. The conjugates were characterized by physico-chemical and immunological assays, including GLC-MS and matrix-assisted laser desorption ionization time-of-flight spectrometry, and immunogenicity in 5- to 6-week-old mice. IgG anti-γdPGA and antiprotein were measured by ELISA. The highest levels of IgG anti-γdPGA were elicited by decamers of γdPGA at 10 –20 mol per protein bound to the N- or C-terminal end. High IgG anti-γdPGA levels were elicited by two injections of 2.5 μg of γdPGA per mouse, whereas three injections were needed to achieve high levels of protein antibodies.rPA was the most effective carrier. Anti-γdPGA induced opsonophagocytic killing ofB. anthracistox–, cap+. γdPGA conjugates may enhance the protection conferred by PA alone. γdPGA-rPA conjugates induced both anti-PA and anti-γdPGA.
The cytoplasmic domain of the Plasmodium falciparum ligand EBA-175 is essential for invasion but not protein trafficking
Authors: Gilberger Tim-Wolf , Thompson Jennifer K. , Reed Michael B. , Good Robert T. , Cowman Alan F.
Published: July 2003

The invasion of host cells by the malaria parasite Plasmodium falciparum requires specific protein–protein interactions between parasite and host receptors and an intracellular translocation machinery to power the process. The transmembrane erythrocyte binding protein-175 (EBA-175) and thrombospondin-related anonymous protein (TRAP) play central roles in this process. EBA-175 binds to glycophorin A on human erythrocytes during the invasion process, linking the parasite to the surface of the host cell. In this report, we show that the cytoplasmic domain of EBA-175 encodes crucial information for its role in merozoite invasion, and that trafficking of this protein is independent of this domain. Further, we show that the cytoplasmic domain of TRAP, a protein that is not expressed in merozoites but is essential for invasion of liver cells by the sporozoite stage, can substitute for the cytoplasmic domain of EBA-175. These results show that the parasite uses the same components of its cellular machinery for invasion regardless of the host cell type and invasive form.
Alternating metabolic pathways in NGF-deprived sympathetic neurons affect caspase-independent death
Authors: Chang Louis K. , Schmidt Robert E. , Johnson Eugene M.
Published: July 2003

Mitochondrial release of cytochrome c in apoptotic cells activates caspases, which execute apoptotic cell death. However, the events themselves that culminate in caspase activation can have deleterious effects because caspase inhibitor–saved cells ultimately die in a caspase-independent manner. To determine what events may underlie this form of cell death, we examined bioenergetic changes in sympathetic neurons deprived of NGF in the presence of a broad-spectrum caspase inhibitor, boc-aspartyl-(OMe)-fluoromethylketone. Here, we report that NGF-deprived, boc-aspartyl-(OMe)-fluoromethylketone–saved neurons rely heavily on glycolysis for ATP generation and for survival. Second, the activity of F0F1 contributes to caspase-independent death, but has only a minor role in the maintenance of mitochondrial membrane potential, which is maintained primarily by electron transport. Third, permeability transition pore inhibition by cyclosporin A attenuates NGF deprivation–induced loss of mitochondrial proteins, suggesting that permeability transition pore opening may have a function in regulating the degradation of mitochondria after cytochrome c release. Identification of changes in caspase inhibitor–saved cells may provide the basis for rational strategies to augment the effectiveness of the therapeutic use of postmitochondrial interventions.
Quantitative quality control in microarray
experiments and the application in data filtering,
normalization and false positive rate prediction
Authors: Wang Xujing , Hessner Martin J. , Wu Yan , Pati Nirupma , Ghosh Soumitra
Published: July 2003

Abstract: Data preprocessing including proper normalization and adequate quality control before complex data mining is crucial for studies using the cDNA microarray technology. We have developed a simple procedure that integrates data filtering and normalization with quantitative quality control of microarray experiments. Previously we have shown that data variability in a microarray experiment can be very well captured by a quality score qcom that is defined for every spot, and the ratio distribution depends on qcom. Utilizing this knowledge, our data-filtering scheme allows the investigator to decide on the filtering stringency according to desired data variability, and our normalization procedure corrects the qcom-dependent dye biases in terms of both the location and the spread of the ratio distribution. In addition, we propose a statistical model for false positive rate determination based on the design and the quality of a microarray experiment. The model predicts that a lower limit of 0.5 for the replicate concordance rate is needed in order to be certain of true positives. Our work demonstrates the importance and advantages of having a quantitative quality control scheme for microarrays.

Contact: xujing@mcw.edu

* To whom correspondence should be addressed.
ESTprep: preprocessing cDNA sequence reads
Authors: Scheetz Todd E. , Trivedi Nishank , Roberts Chad A. , Kucaba Tamara , Berger Brian , Robinson Natalie L. , Birkett Clayton L. , Gavin Allen J. , O’Leary Brian , Braun Terry A. , Bonaldo Maria F. , Robinson John P. , Sheffield Val C. , Soares Marcelo B. , Casavant Thomas L.
Published: July 2003

Motivation: High accuracy of data always governs the large-scale gene discovery projects. The data should not only be trustworthy but should be correctly annotated for various features it contains. Sequence errors are inherent in single-pass sequences such as ESTs obtained from automated sequencing. These errors further complicate the automated identification of EST-related sequencing. A tool is required to prepare the data prior to advanced annotation processing and submission to public databases.

Results: This paper describes ESTprep, a program designed to preprocess expressed sequence tag (EST) sequences. It identifies the location of features present in ESTs and allows the sequence to pass only if it meets various quality criteria. Use of ESTprep has resulted in substantial improvement in accurate EST feature identification and fidelity of results submitted to GenBank.

Availability: The program is freely available for download from http://genome.uiowa.edu/pubsoft/software.html

Contact: tscheetz@eng.uiowa.edu

* To whom correspondence should be addressed.
Design and assessment of a fast algorithm for
identifying specific probes for human and mouse genes
Authors: Chang Pei-chin , Peck Konan
Published: July 2003

Motivation: Mammalian genomes are highly complex. To identify the unique sequences of each gene in a mammalian gene database containing tens of thousands of DNA sequences is a computation intensive task. With the advent of parallel genetic analysis methods such as microarrays and the availability of more and more whole genome sequences of organisms, an algorithm allowing speedy identification of the unique gene probes for functional studies of individual genes will be a very useful tool.

Results: We have developed a fast algorithm as well as a software program based on the algorithm for identifying gene specific probes of complex organisms. The algorithm was applied to the assemblies of gene sequences and was highly efficient for large databases such as the TIGR human THC and mouse TC databases. The results were assessed with the BLAST sequence alignment software. Two probe data sets have been compiled to contain specific probes for around 100 000 putative human gene transcripts and 70 000 putative mouse gene transcripts.

Availability: The gene specific probes for the putative human and mouse genes referenced in the TIGR gene indices are available at: ftp://genestamp.ibms.sinica.edu.tw/pub/SpecificP/. The software program and the source codes are available upon request.

Contact: konan@ibms.sinica.edu.tw

* To whom correspondence should be addressed.
Noise sampling method: an ANOVA approach
allowing robust selection of differentially regulated
genes measured by DNA microarrays
Authors: Draghici Sorin , Kulaeva Olga , Hoff Bruce , Petrov Anton , Shams Soheil , Tainsky Michael A.
Published: July 2003

Motivation: A crucial step in microarray data analysis is the selection of subsets of interesting genes from the initial set of genes. In many cases, especially when comparing a specific condition to a reference, the genes of interest are those which are differentially expressed. Two common methods for gene selection are: (a) selection by fold difference (at least n fold variation) and (b) selection by altered ratio (at least n standard deviations away from the mean ratio).

Results: The novel method proposed here is based on ANOVA and uses replicate spots to estimate an empirical distribution of the noise. The measured intensity range is divided in a number of intervals. A noise distribution is constructed for each such interval. Bootstrapping is used to map the desired confidence levels from the noise distribution corresponding to a given interval to the measured log ratios in that interval. If the method is applied on individual arrays having replicate spots, the method can calculate an overall width of the noise distribution which can be used as an indicator of the array quality. We compared this method with the fold change and unusual ratio method. We also discuss the relationship with an ANOVA model proposed by Churchill et al.

In silico experiments were performed while controlling the degree of regulation as well as the amount of noise. Such experiments show the performance of the classical methods can be very unsatisfactory. We also compared the results of the 2-fold method with the results of the noise sampling method using pre and post immortalization cell lines derived from the MDAH041 fibroblasts hybridized on Affymetrix GeneChip arrays. The 2-fold method reported 198 genes as upregulated and 493 genes as downregulated. The noise sampling method reported 98 gene upregulated and 240 genes downregulated at the 99.99% confidence level. The methods agreed on 221 genes downregulated and 66 genes upregulated. Fourteen genes from the subset of genes reported by both methods were all confirmed by Q-RT-PCR. Alternative assays on various subsets of genes on which the two methods disagreed suggested that the noise sampling method is likely to provide fewer false positives.

Contact: sod@cs.wayne.edu

* To whom correspondence should be addressed.

† The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
A comparison of physical mapping algorithms
based on the maximum likelihood model
Authors: Huang Jinling , Bhandarkar Suchendra M.
Published: July 2003

Motivation: Physical mapping of chromosomes using the maximum likelihood (ML) model is a problem of high computational complexity entailing both discrete optimization to recover the optimal probe order as well as continuous optimization to recover the optimal inter-probe spacings. In this paper, two versions of the genetic algorithm (GA) are proposed, one with heuristic crossover and deterministic replacement and the other with heuristic crossover and stochastic replacement, for the physical mapping problem under the maximum likelihood model. The genetic algorithms are compared with two other discrete optimization approaches, namely simulated annealing (SA) and large-step Markov chains (LSMC), in terms of solution quality and runtime efficiency.

Results: The physical mapping algorithms based on the GA, SA and LSMC have been tested using synthetic datasets and real datasets derived from cosmid libraries of the fungus Neurospora crassa. The GA, especially the version with heuristic crossover and stochastic replacement, is shown to consistently outperform the SA-based and LSMC-based physical mapping algorithms in terms of runtime and final solution quality. Experimental results on real datasets and simulated datasets are presented. Further improvements to the GA in the context of physical mapping under the maximum likelihood model are proposed.

Availability: The software is available upon request from the first author.

Contact: tupistra@yahoo.com

* To whom correspondence should be addressed.

† Present address: Center for Tropical and Emerging Global Diseases, 623 Biological Science Building, University of Georgia, Athens, GA 30602, USA.
On the use of permutation in and the performance
of a class of nonparametric methods to detect
differential gene expression
Authors: Pan Wei
Published: July 2003

Motivation: Recently a class of nonparametric statistical methods, including the empirical Bayes (EB) method, the significance analysis of microarray (SAM) method and the mixture model method (MMM), have been proposed to detect differential gene expression for replicated microarray experiments conducted under two conditions. All the methods depend on constructing a test statistic Z and a so-called null statistic z. The null statistic z is used to provide some reference distribution for Z such that statistical inference can be accomplished. A common way of constructing z is to apply Z to randomly permuted data. Here we point our that the distribution of z may not approximate the null distribution of Z well, leading to possibly too conservative inference. This observation may apply to other permutation-based nonparametric methods. We propose a new method of constructing a null statistic that aims to estimate the null distribution of a test statistic directly.

Results: Using simulated data and real data, we assess and compare the performance of the existing method and our new method when applied in EB, SAM and MMM. Some interesting findings on operating characteristics of EB, SAM and MMM are also reported. Finally, by combining the idea of SAM and MMM, we outline a simple nonparametric method based on the direct use of a test statistic and a null statistic.

Contact: weip@biostat.umn.edu
2HAPI: a microarray data analysis system
Authors: Fink J. Lynn , Drewes Scott , Patel Hiren , Welsh John B. , Masys Daniel R. , Corbeil Jacques , Gribskov Michael
Published: July 2003

Summary: 2HAPI (version 2 of High density Array Pattern Interpreter) is a web-based, publicly-available analytical tool designed to aid researchers in microarray data analysis. 2HAPI includes tools for searching, manipulating, visualizing, and clustering the large sets of data generated by microarray experiments. Other features include association of genes with NCBI information and linkage to external data resources. Unique to 2HAPI is the ability to retrieve upstream sequences of co-regulated genes for promoter analysis using MEME (Multiple Expectation-maximization for Motif Elicitation)

Availability: 2HAPI is freely available at http://array.sdsc.edu. Users can try 2HAPI anonymously with pre-loaded data or they can register as a 2HAPI user and upload their data.

Contact: gribskov@sdsc.edu

* To whom correspondence should be addressed.
GeneTRACE–reconstruction of gene content of ancestral species
Authors: Kunin Victor , Ouzounis Christos A.
Published: July 2003

While current computational methods allow the reconstruction of individual ancestral protein sequences, reconstruction of complete gene content of ancestral species is not yet an established task. In this paper, we describe GeneTrace, an efficient linear-time algorithm that allows the reconstruction of evolutionary history of individual protein families as well as the complete gene content of ancestral species. The performance of the method was validated with a simulated evolution program called SimulEv. Our results indicate that given a set of correct phylogenetic profiles and a correct species tree, ancestral gene content can be reconstructed with sensitivity and selectivity of more than 90%. SimulEv simulations were also used to evaluate performance of the reconstruction of gene content-based phylogenetic trees, suggesting that these trees may be accurate at the terminal branches but suffer from long branch attraction near the root of the tree.

Contact: ouzounis@ebi.ac.uk

* To whom correspondence should be addressed.
POAVIZ: a Partial Order Multiple Sequence Alignment Visualizer
Authors: Grasso Catherine , Quist Michael , Ke Kevin , Lee Christopher
Published: July 2003

Summary: POAVIZ creates a visualization of a multiple sequence alignment that makes clear the overall structure of how sequences match and diverge in the alignment. POAVIZ can construct visualizations from any multiple sequence alignment source (e.g. PIR and CLUSTAL formats), and is valuable for revealing complex branching structure (such as domains, large-scale insertions / deletions or recombinations), especially in partnership with the Partial Order Alignment (POA) multiple sequence alignment program.

Availability: The Partial Order multiple sequence Alignment Visualizer (POAVIZ) program is available at http://www.bioinformatics.ucla.edu/poa

Contact: leec@mbi.ucla.edu

* To whom correspondence should be addressed.
Estimation of transformation parameters for microarray data
Authors: Durbin Blythe , Rocke David M.
Published: July 2003

Motivation and Results: Durbin et al. (2002), Huber et al. (2002) and Munson (2001) independently introduced a family of transformations (the generalized-log family) which stabilizes the variance of microarray data up to the first order. We introduce a method for estimating the transformation parameter in tandem with a linear model based on the procedure outlined in Box and Cox (1964). We also discuss means of finding transformations within the generalized-log family which are optimal under other criteria, such as minimum residual skewness and minimum mean-variance dependency.

Availability: R and Matlab code and test data are available from the authors on request.

Contact: bpdurbin@ucdavis.edu

* To whom correspondence should be addressed.
SKN-1 linksC. elegansmesendodermal specification to a conserved oxidative stress response
Authors: An Jae Hyung , Blackwell T. Keith
Published: July 2003

During the earliest stages ofCaenorhabditis elegansembryogenesis, the transcription factor SKN-1 initiates development of the digestive system and other mesendodermal tissues. Postembryonic SKN-1 functions have not been elucidated. SKN-1 binds to DNA through a unique mechanism, but is distantly related to basic leucine-zipper proteins that orchestrate the major oxidative stress response in vertebrates and yeast. Here we show that despite its distinct mode of target gene recognition, SKN-1 functions similarly to resist oxidative stress inC. elegans. During postembryonic stages, SKN-1 regulates a key Phase II detoxification gene through constitutive and stress-inducible mechanisms in the ASI chemosensory neurons and intestine, respectively. SKN-1 is present in ASI nuclei under normal conditions, and accumulates in intestinal nuclei in response to oxidative stress.skn-1mutants are sensitive to oxidative stress and have shortened lifespans. SKN-1 represents a connection between developmental specification of the digestive system and one of its most basic functions, resistance to oxidative and xenobiotic stress. This oxidative stress response thus appears to be both widely conserved and ancient, suggesting that the mesendodermal specification role of SKN-1 was predated by its function in these detoxification mechanisms.
E. coli Selection of Human Genes Encoding Secreted and Membrane Proteins Based on cDNA Fusions to a Leaderless β-Lactamase Reporter
Authors: Tan Ruoying , Jiang Xin , Jackson Alan , Jin Pei , Yang Junming , Lee Ernestine , Duggan Brendan , Stuve Laura L. , Fu Glenn K.
Published: July 2003

Although several signal peptide-trapping methods have been devised and used to detect signal sequences, none have relied on using E.coli to identify eukaryotic proteins with signal peptides. Here, we describe a system for selecting human secreted and membrane proteins in E. coli followed by the direct validation of secretion in human cells. The method is based on cDNA fusions to a leaderless β-lactamase reporter gene to isolate clones encoding signal peptides of human genes. We found that β-lactamase fusion proteins carrying a eukaryotic signal peptide at its N-terminus were able to direct their export into the periplasm in E. coli to confer survival upon challenge with carbenicillin. When libraries constructed from 5′ end-enriched cDNAs fused to β-lactamase were screened in E.coli, approximately 0.5%–1% of the cDNAs are selected, and over half of the surviving clones were found to encode for secreted fusion proteins when tested in human cells. These clones were sequenced and shown to represent human genes encoding signal peptides of secreted and membrane proteins. We conclude that this is an efficient and effective strategy to easily enrich cDNA libraries for the identification of novel genes likely to encode secreted enzymes, growth factors, and receptors.
The Origin of Human Chromosome 1 and Its Homologs in Placental Mammals
Authors: Murphy William J. , Frönicke Lutz , O'Brien Stephen J. , Stanyon Roscoe
Published: July 2003

Developing ordered gene maps from multiple mammalian species coupled with chromosome-painting data provide a powerful resource for resolving the evolutionary history of chromosomes and whole genomes. In this work, we recapitulate the evolutionary history of human chromosome 1 and its homologs in placental mammals, putatively the largest physical unit in the ancestral placental genome. Precise definition of translocation exchange breakpoints in human, carnivore, cetartiodactyl, and rodent-ordered gene maps demonstrate that chromosome breakpoints, previously considered as equivalent, actually represent distinct chromosome positions and exchange events. Multidirectional chromosome painting, using probes from homologs to chromosome 1 in seven mammal species from six orders of placental mammals, confirm the gene-mapping results and indicate that the multiple human chromosome 1 homologs in these species are derived from independent fissions of a single ancestral chromosome. Chromosome painting using human chromosome 1 probes identifies a single human chromosome 1 homolog in phylogenetically distant taxa, the two-toed sloth, cetaceans, and higher primates. The diverse phylogenetic occurrence of a single Hsa1 synteny among the major clades of placental mammals suggests that human chromosome 1 represents an intact ancestral chromosome, which was variously fissioned in the majority of placental species. We find that the number of human chromosome 1 fissions in a specific lineage reflects its general rate of genomic evolution. Further, historic chromosome exchange appears to have been disproportionately clustered in two breakpoint hotspots on the long arm.
Polymer hydration and microphase decomposition in poly(N-vinylcaprolactam)–water complex
Authors: Lebedev Vassili , Török Gyula , Cser László , Treimer Wolfgang , Orlova Diana , Sibilev Avgustin
Published: July 2003

Poly(N-vinylcaprolactam) (PVCL) is a synthetic analogue of biomolecules (enzymes, proteins). It demonstrates a specific hydration and undergoes a coil–globule transition. The PVCL–D2O system (PVCL massM= 106) has been investigated by small-angle neutron scattering (SANS) atT= 296–316 K to identify the structural features of the collapse at concentrationC= 0.5 wt% near the threshold of the coil overlap. (The collapse leads to the segregation of the phase enriched with polymer atT> 305 K). The SANS experiments atq= 0.1–5 nm−1(scales from monomer unit to globule gyration radiusRG≃ 16 nm) have revealed a stretched coil–globule transformation in the range 305–309 K. Using high-resolution SANS (q= 0.002–0.02 nm−1) the globule association to form fractal structures (sponge-like) of surface dimensionDF≃ 2.4–2.6 was examined. The coexistence of globules and disordered chains (regions ∼5–10 nm) was found. The growth of the content of globular phase was induced by the conformational transition in disordered molecular fragments from coiled (dimensionD≃ 1.8) to stretched chains (D≃ 1.2).
Transformation of cubic symmetry for spherical microdomains from face-centred to body-centred cubic upon uniaxial elongation in an elastomeric triblock copolymer
Authors: Imaizumi K. , Ono T. , Kota T. , Okamoto S. , Sakurai S.
Published: July 2003

Experimental observation of the transformation of cubic symmetry from face-centred cubic (f.c.c.) to body-centred cubic (b.c.c.) for spherical microdomains upon uniaxial stretching of poly(1,3-cyclohexadiene)-block-poly(ethylene-co-but-1-ene)-block-poly(1,3-cyclohexadiene) triblock copolymer, having φPCHD= 0.293,Mn= 5.73 × 104,Mw/Mn= 1.09, is reported. First, the sample was subjected to flow treatment at 493 K for 2 h; then it was annealed at 473 K for 2 h to prepare the f.c.c. structure. The sample was subsequently subjected to uniaxial stretching. After the load was completely removed, small-angle X-ray scattering measurements were conducted. It was found that the f.c.c. packing was transformed to the well ordered b.c.c. packing upon uniaxial stretching.
Singular value decomposition analysis of time-resolved small-angle X-ray scattering during morphological transition in a block copolymer
Authors: Okamoto Shigeru , Sakurai Shinichi
Published: July 2003

Time-resolved small-angle X-ray scattering (TR-SAXS) studies of the structural changes in a block copolymer after a temperature jump are reported. The sample used was a polystyrene-block-poly(ethylene-alt-butylene)-block-polystyrene (SEBS) triblock copolymer, which has a number-average molecular weight of 54000 g mol−1and a volume fraction of polystyrene of 0.227. The film specimen was prepared by the solution-cast method using a selective solvent. The as-cast specimen with lamellar microdomains underwent the temperature jump from 363 to 403 K and the morphological transition from lamellae to cylinders was observed as a function of time by the TR-SAXS technique. The singular value decomposition (SVD) analysis was performed on the scattering profiles. This analysis strongly suggested the existence of a third basis component of the X-ray scattering profiles, thus supporting that there is an intermediate state during the transition from lamellae to cylinders.
Co-crystallization of poly(ethylene–butene) copolymers and paraffin molecules in decane studied with small-angle neutron scattering
Authors: Radulescu A. , Schwahn D. , Richter D. , Fetters L .J.
Published: July 2003

PEB-nsemicrystalline poly(ethylene–butene) random copolymers may become important in industrial applications because of their capability to modify the paraffin crystals and to improve the viscoelastic properties of crude oil and refined fuel. The copolymer–paraffin interaction is rather complex and is not yet understood. Therefore, these polymers may also be of much interest in basic research. Systematic small-angle neutron scattering investigations of different polymer–paraffin systems have shown that PEB-ncopolymers are selective in their paraffin-modification capacity, depending on the crystalline degree which is tuned by the number `n' of ethyl side branches/100 backbone C atoms. Two mechanisms of polymer–paraffin interaction have been identified: on the one hand, co-crystallization of the paraffin and copolymer within thin platelets occurs as a consequence of a good fit between the self-assembling properties of the investigated polymer/paraffin pairs (PEB-7.5/C36and PEB-11/C24); on the other hand, primordial polymer aggregates act as a template for a subsequent paraffin crystallization when the polymer has a higher self-assembling point (PEB-7.5/C24) than the paraffin. Both mechanisms were found for the PEB-7.5/C30mixture.
Microstructure of radiation-damaged zircon under pressure
Authors: Ríos Susana , Boffa-Ballaran Tiziana
Published: July 2003

Radiation-damaged zircons have been studied at high pressures, up to 7 GPa, by means of single-crystal X-ray diffraction at room temperature. The zircons studied contained high fractions of amorphous material (65 and 85%, respectively). Peak profiles of selected Bragg reflections at room pressure give evidence of the complex microstructure of defective crystalline regions. A differential stress of ∼20 GPa is found between expanded and compressed regions. Two clear stages are observed as a function of pressure: (i) below 3 GPa, diffraction maxima do not show significant changes; (ii) above 3 GPa, a simultaneous increase in peak intensity and decrease in mosaic spread is observed. The effects are attributed to reorientation of crystalline domains within the amorphous matrix. The starting peak profile is recovered after releasing pressure, implying that no significant defect healing is induced in this pressure range, and that all observed effects are reversible. Results are interpreted in terms of the non-uniform structure of amorphous cascades.
NEUTRON: a program for computing phonon extinction rules of inelastic neutron scattering and thermal diffuse scattering experiments
Authors: Kirov Asen K. , Aroyo Mois I. , Perez-Mato J. Manuel
Published: July 2003

NEUTRONis a computer program for calculating the phonon extinction rules for inelastic neutron scattering experiments. Given the space group and the phonon symmetry specified by the wavevector, the program examines the inelastic neutron scattering activity of the corresponding phonons for all possible types of scattering vectors. The systematic selection rules are also useful in the interpretation of the results of thermal diffuse scattering.NEUTRONforms part of the Bilbao Crystallographic server (http://www.cryst.ehu.es) and can be usedviathe Internet from any computer with a Web browser.
Image analysis of transmission electron micrographs of semicrystalline polymers: a comparison with X-ray scattering results
Authors: Haubruge H. G. , Gallez X. A. , Nysten B. , Jonas A. M.
Published: July 2003

Image analysis of semi-crystalline polymer systems in reciprocal space allows quantitative measurement of characteristic periodicities of the material. This paper proposes numerical techniques for the computation of power spectral densities (PSD) and correlation functions, appropriate to this objective, along with a theoretical justification. These methods are applied to transmission electron micrographs of isotactic polypropylene (iPP) and poly(ethylene terephthalate) (PET). Measured characteristic periodicities arise from electronic contrast between crystalline and stained amorphous phases. They correlate well with results obtained by small-angle X-ray scattering (SAXS) on non-stained samples.
In situhigh-temperature powder diffraction study of reversible phase transitions in decagonal Al71.2Co12.8Ni16
Authors: Soltmann Christian , Beeli Conradin , Lück Reinhard , Gander Walter
Published: July 2003

This experimental work is aimed at confirming and broadening findings of former investigations into the typeI↔S1 phase transition in Al–Co–Ni quasicrystals.In situhigh-temperature synchrotron radiation measurements were carried out on Al71.2Co12.8Ni16powder samples. The cell parameters were precisely determined at various temperatures in the range 290–1110 K. The data provided a new extended insight into the thermal expansion of Al71.2Co12.8Ni16and into fundamental properties of the phase transition.
Synchrotron texture analysis with area detectors
Authors: Wenk H.-R. , Grigull S.
Published: July 2003

The wide availability of X-ray area detectors provides an opportunity for using synchrotron radiation based X-ray diffraction for the determination of preferred crystallite orientation in polycrystalline materials. These measurements are very fast compared to other techniques. Texture is immediately recognized as intensity variations along Debye rings in diffraction images, yet in many cases this information is not used because the quantitative treatment of texture information has not yet been developed into a standard technique. In special cases it is possible to interpret the texture information contained in these intensity variations intuitively. However, diffraction studies focused on the effects of texture on materials properties often require the full orientation distribution function (ODF) which can be obtained from spherical tomography analysis. In cases of high crystal symmetry (cubic and hexagonal) an approximation to the full ODF can be reconstructed from single diffraction images, as is demonstrated for textures in rolled copper and titanium sheets. Combined with area detectors, the reconstruction methods make the measurements fast enough to study orientation changes during phase transformations, recrystallization and deformationin situ, and even in real time, at a wide range of temperature and pressure conditions. The present work focuses on practical aspects of texture measurement and data processing procedures to make the latter available for the growing community of synchrotron users. It reviews previous applications and highlights some opportunities for synchrotron texture analysis based on case studies on different materials.
Structural analysis of excess-anion C-type rare earth oxide: a case study with Gd1−xCexO1.5+x/2(x= 0.20 and 0.40)
Authors: Grover V. , Achary S. N. , Tyagi A. K.
Published: July 2003

Structural analysis of anion-rich C-type Gd2O3was carried by the Rietveld refinement of the powder X-ray diffraction data for compositions Gd0.8Ce0.2O1.60and Gd0.6Ce0.4O1.70. Both compounds have a body-centred cubic lattice (space groupIa\bar{3}, No. 206,Z= 32) with unit-cell parameters of 10.8488 (1) and 10.8542 (1) Å, respectively. Both of these compounds are iso-structural with the C-type rare earth oxides, with excess anions as required for charge balance. The structural analysis reveals that there are two different kinds of metal ion site, namely 8b(M1) and 24d(M2), and two different kinds of anion sites, namely 48e(O1) and 16c(O2). The excess anions occupy the 16c(xxx) sites. The two metal ions each form an approximately eightfold-coordination polyhedron with O1 and O2. The details of these two compositions are explained and compared with both the CeO2structure and the Gd2O3structure,i.e.the end member.
Effects of the choice of different ionization level for scattering curves and correction for small preferred orientation in Rietveld refinement: the MgAl2O4test case
Authors: Ballirano Paolo
Published: July 2003

The effects of the choice of oxygen scattering curves with different ionization levels and of the number of spherical harmonics terms used to correct for preferred orientation are discussed in the case of the Rietveld refinement of MgAl2O4spinel. Results indicate that Rietveld refinements, and not only single-crystal analyses, are influenced by the choice of the scattering curves, at least in the case of very simple ionic structures. Improvements are observed both in agreement indices and in displacement parameter modelling by the use of an almost fully ionized model. On the contrary, the choice of the order of spherical harmonics prevalently affects the fractionalucoordinate.
Precise measurement of the lattice parameters of α-Al2O3in the temperature range 4.5–250 K using the Mössbauer wavelength standard
Authors: Lucht M. , Lerche M. , Wille H.-C. , Shvyd'ko Yu. V. , Rüter H. D. , Gerdau E. , Becker P.
Published: July 2003

The lattice parameters of α-Al2O3have been measured in a temperature range from 4.5 to 250 K with a relative accuracy of better than 6 × 10−6. The experimental method uses Bragg backscattering and the recently proposed Mössbauer wavelength standard,i.e.the wavelength λM= 86.025474 (16) pm of the nuclear resonance radiation of57Fe (Shvyd'koet al., 2000), which has previously been applied successfully to measure the lattice parameters of α-Al2O3at temperatures between 286 and 374 K (Shvyd'koet al., 2002). The experimental data in the range from 4.5 to 374 K are consistent with the Debye model of thermal expansion. At 4.5 K, the thermal expansion coefficient is as low as 1.2 (9) × 10−10 K−1in theadirection.
Generation of grain maps by an algebraic reconstruction technique
Authors: Poulsen H. F. , Fu Xiaowei
Published: July 2003

A reconstruction method is presented for the generation of three-dimensional maps of the grain boundaries within powders or polycrystals. The grains are assumed to have a mosaic spread below 1°. They are mapped layer by layer in a non-destructive way by diffraction with hard X-rays. First the diffraction spots are sorted with respect to grain of origin by the indexing programGRAINDEX. Next for each grain the reconstruction is performed byART– an iterative algebraic algorithm. The method is optimized by simulations. It is verified by a 50 keV study on one embedded layer in an aluminium specimen. The layer comprises ∼50 grain sections of an average size of 100 µm. Based on the use of five reflections per grain, a resolution of ∼5 µm is inferred.