bluuebunny/crossref_metadata_2025 huggingface dataset:
The impact of HIV-related neuropsychological dysfunction
on driving behavior
Authors: MARCOTTE THOMAS D. , HEATON ROBERT K. , WOLFSON TANYA , TAYLOR MICHAEL J. , ALHASSOON OMAR , ARFAA KAIVON , ELLIS RONALD J. , GRANT IGOR , GROUP THE HNRC
Published: July 2002

The following is a correction for an error that occurred in the Journal of the International Neuropsychological Society, Vol. 6, No. 3. The error occurred in the article titled “Personality change disorder in children and adolescents following traumatic brain injury,” pp. 279–289, by Max et al. On page 285, under the subheading “Injury Factors,” beginning with the second sentence in the first paragraph, the statement should read:

Visual inspection of the distribution of PC relative to lowest post-resuscitation GCS scores revealed that a cut-off of lowest post-resuscitation GCS score of 4 or less versus more than 4 yielded a sensitivity for a diagnosis of persistent PC of 9/14 (64.3%), specificity of 18/23 (78.3%), and a positive predictive value of 0.64 (9.14).

A cut-off of duration of impaired consciousness of 100 hr or less versus more than 100 hr yielded a sensitivity for a diagnosis of persistent PC of 11/14 (78.6%), specificity of 20/23 (87.0%), and a positive predictive value (PPV) of 0.79 (11/14).
Neuropsychological performance in body dysmorphic disorder
Authors: Hanes Karl R.
Published: July 2002

Fourteen patients with body dysmorphic disorder
(BDD) were assessed with neuropsychological measures, including
tests of executive, mnestic, and motor functions. Performance
in these patients was compared to 10 patients with obsessive-compulsive
disorder (OCD), 14 patients with schizophrenia, and 24
normal controls. Findings indicated normal performance
of the BDD group on measures of mnestic and motor function,
but poor performance of this group on tests of executive
function (p < .05). The overall performance
of the BDD and OCD groups on the neuropsychological measures
was similar, while the schizophrenic groups showed a wider
spectrum of neuropsychological deficits to these groups.
These findings are discussed in terms of current theories
of executive functions and the possible relationship between
BDD and OCD. (JINS, 1998, 4, 167–171.)
The role of syntactic complexity in training wh-movement
structures in agrammatic aphasia: Optimal order for promoting
generalization
Authors: THOMPSON CYNTHIA K. , BALLARD KIRRIE J. , SHAPIRO LEWIS P.
Published: July 2002

This study examined the postulate that training
production of syntactically complex sentences results in
generalization to less complex sentences that have processes
in common with treated structures. Three agrammatic aphasic
patients were trained to produce wh-movement structures,
object clefts and/or object extracted who-questions,
while generalization between these structures was tested.
One NP-movement structure, passive sentences, also was
tested for control purposes. Wh-movement occurs
from the direct object position to specifier position
in the complementizer phrase [SPEC, CP] for both
wh-movement structures. In who-questions
movement occurs in the matrix sentence, whereas, in object
clefts movement occurs within an embedded relative clause,
rendering them the most complex. Results showed robust
generalization effects from object clefts to matrix who-question
for 1 participant (D.L.); however, no generalization was
noted from who-questions to object clefts for
another (F.P.), and 1 participant (C.H.) showed acquisition
of who-questions, but not object clefts, during
the baseline condition without direct treatment. As expected,
none of the participants showed improved production of
passives. These findings supported those derived from our
previous studies, indicating that generalization is enhanced
not only when target structures are related along dimensions
articulated by linguistic theory, but also when the direction
of treatment is from more to less complex structures. The
present findings also support proposals that projections
of higher levels in the syntactic treatment are dependent
on successful projection of lower levels. For our participants,
training movement within CP in a lower (embedded) clause
resulted in their ability to project to CP at higher levels.
(JINS, 1998, 4, 661–674.)
Construction of a fund for the sharing of benefits from the utilization of plant genetic resources for food and agriculture
Authors: COOPER JOSEPH C.
Published: July 2002

A major issue in international multilateral negotiations is the creation of a fund for the fair and equitable sharing of benefits arising out of the utilization of plant genetic resources for food and agriculture (PGRFA). This paper provides a conceptual understanding of the economic value of PGRFA, identifies proxies for this value that can be used to determine the relative contribution of each country to the benefit-sharing fund, and evaluates the suitability of each proxy to this task.
Separation anxiety: metaphoric transmutations from a paradoxical biological instrument, or: What is a cactus doing in

our concert hall?
Authors: Rudy Paul
Published: July 2002

In its original rendition, Degrees of Separation: “Grandchild of Tree” (1998) is performed with cactus, outboard digital effects, and CD playback, with simple lighting. The work is a metaphor which portrays subtle transformations (or transmutations) in human existence precipitated by pervasive new technology. A new version consists of a performance with a video component and all electronics fully automated in MAX/MSP on a Macintosh Powerbook. Development of this work, and subsequent versions, have proven invaluable for my own approach to the music I compose, and for the understanding of my position in the contemporary world of computers, technology and art. This paper attempts to describe these discoveries through outlining the levels of symbolism and metaphor in the work as realised through source abstraction (both visually and aurally), spatialisation and (re-)contextualisation. It begins with the question: What is a cactus doing in the concert hall?
EVOLUTION AND TIME HORIZONS IN AN AGENT-BASED STOCK MARKET
Authors: LeBaron Blake
Published: July 2002

Recent research has shown the importance of time horizons in models of learning in finance. The dynamics of how agents adjust to believe that the world around them is stationary may be just as crucial in the convergence to a rational expectations equilibrium as getting parameters and model specifications correct in the learning process. This paper explores the process of this evolution in learning and time horizons in a simple agent-based financial market. The results indicate that, although the simple model structure used here replicates usual rational expectations results with long-horizon agents, the route to evolving a population of both long- and short-horizon agents to long horizons alone may be difficult. Furthermore, populations with both short- and long-horizon agents increase return variability, and leave patterns in volatility and trading volume similar to actual financial markets.
Did dinosaurs invent flowers? Dinosaur—angiosperm coevolution revisited
Authors: BARRETT PAUL M. , WILLIS KATHERINE J.
Published: July 2002

Angiosperms first appeared in northern Gondwana during the Early Cretaceous, approximately 135 million years ago. Several authors have hypothesised that the origin of angiosperms, and the tempo and pattern of their subsequent radiation, was mediated by changes in the browsing behaviour of large herbivorous dinosaurs (sauropods and ornithischians). Moreover, the taxonomic and ecological radiation of angiosperms has been associated with the evolution of complex jaw mechanisms among ornithischian dinosaurs. Here, we review critically the evidence for dinosaur–angiosperm interactions during the Cretaceous Period, providing explicit spatiotemporal comparisons between evolutionary and palaeoecological events in both the dinosaur and angiosperm fossil records and an assessment of the direct and indirect evidence for dinosaur diets. We conclude that there are no strong spatiotemporal correlations in support of the hypothesis that dinosaurs were causative agents in the origin of angiosperms; however, dinosaur–angiosperm interactions in the Late Cretaceous may have resulted in some coevolutionary interactions, although direct evidence of such interactions is scanty at present. It is likely that other animal groups (insects, arboreal mammals) had a greater impact on angiosperm diversity during the Cretaceous than herbivorous dinosaurs. Elevated levels of atmospheric CO2might have played a critical role in the initial stages of the angiosperm radiation.
Activation of the Notch-regulated transcription factor CBF1/RBP-Jκ through the 13SE1A oncoprotein
Authors: Ansieau Stéphane , Strobl Lothar J. , Leutz Achim
Published: July 2002

Signaling through the Notch pathway controls cell growth and differentiation in metazoans. Following binding of its ligands, the intracellular part of the cell surface Notch1 receptor (Notch1-IC) is released and translocates to the nucleus, where it alters the function of the DNA-binding transcription factor CBF1/RBP-Jκ. As a result, CBF1/RBP-Jκ is converted from a repressor to an activator of gene transcription. Similarly, the Epstein Barr viral oncoprotein EBNA2, which is required for B-cell immortalization, activates genes through CBF1. Moreover, the TAN-1 and int-3 oncogenes represent activated versions of Notch1 and Notch4, respectively. Here, we show that the adenoviral oncoprotein 13S E1A also binds to CBF1/RBP-Jκ, displaces associated corepressor complexes, and activates CBF1/RBP-Jκ–dependent gene expression. Our results suggest that the central role of the Notch–CBF1/RBP-Jκ signaling pathway in cell fate decisions renders it susceptible to pathways of viral replication and oncogenic conversion.
Nf2 gene inactivation in arachnoidal cells is rate-limiting for meningioma development in the mouse
Authors: Kalamarides Michel , Niwa-Kawakita Michiko , Leblois Hélène , Abramowski Vincent , Perricaudet Michel , Janin Anne , Thomas Gilles , Gutmann David H. , Giovannini Marco
Published: July 2002

Biallelic NF2 gene inactivation is common in sporadic and in neurofibromatosis type 2 (NF2)-related meningiomas. We show that, beginning at four months of age, thirty percent of mice with arachnoidal cell Cre-mediated excision of Nf2 exon 2 developed a range of meningioma subtypes histologically similar to the human tumors. Additional hemizygosity for p53 did not modify meningioma frequency or progression suggesting that Nf2 andp53 mutations do not synergize in meningeal tumorigenesis. This first mouse model initiated with a genetic lesion found in human meningiomas provides a powerful tool for investigating tumor progression and for the preclinical evaluation of therapeutic interventions.
Axin-mediated CKI phosphorylation of β-catenin at Ser 45: a molecular switch for the Wnt pathway
Authors: Amit Sharon , Hatzubai Ada , Birman Yaara , Andersen Jens S. , Ben-Shushan Etti , Mann Matthias , Ben-Neriah Yinon , Alkalay Irit
Published: July 2002

The Wnt pathway controls numerous developmental processes via the β-catenin–TCF/LEF transcription complex. Deregulation of the pathway results in the aberrant accumulation of β-catenin in the nucleus, often leading to cancer. Normally, cytoplasmic β-catenin associates with APC and axin and is continuously phosphorylated by GSK-3β, marking it for proteasomal degradation. Wnt signaling is considered to prevent GSK-3β from phosphorylating β-catenin, thus causing its stabilization. However, the Wnt mechanism of action has not been resolved. Here we study the regulation of β-catenin phosphorylation and degradation by the Wnt pathway. Using mass spectrometry and phosphopeptide-specific antibodies, we show that a complex of axin and casein kinase I (CKI) induces β-catenin phosphorylation at a single site: serine 45 (S45). Immunopurified axin and recombinant CKI phosphorylate β-catenin in vitro at S45; CKI inhibition suppresses this phosphorylation in vivo. CKI phosphorylation creates a priming site for GSK-3β and is both necessary and sufficient to initiate the β-catenin phosphorylation–degradation cascade. Wnt3A signaling and Dvl overexpression suppress S45 phosphorylation, thereby precluding the initiation of the cascade. Thus, a single, CKI-dependent phosphorylation event serves as a molecular switch for the Wnt pathway.
The proteasome regulates the UV-induced activation of the AP-1-like transcription factor Gcn4
Authors: Stitzel Michael L. , Durso Robert , Reese Joseph C.
Published: July 2002

The proteasome is well known for its regulation of the cell cycle and degradation of mis-folded proteins, yet many of its functions are still unknown. We show that RPN11, a gene encoding a subunit of the regulatory cap of the proteasome, is required for UV-stimulated activation of Gcn4p target genes, but is dispensable for their activation by the general control pathway. We provide evidence thatRPN11 functions downstream of RAS2, and show that mutation of two additional proteasome subunits results in identical phenotypes. Our analysis defines a novel function of the proteasome: regulation of the RAS- and AP-1 transcription factor-dependent UV resistance pathway.
BH3-only proteins that bind pro-survival Bcl-2 family members fail to induce apoptosis in the absence of Bax and Bak
Authors: Zong Wei-Xing , Lindsten Tullia , Ross Andrea J. , MacGregor Grant R. , Thompson Craig B.
Published: July 2002

The BH3-only proteins Bim and Bad bind to the antiapoptotic Bcl-2 proteins and induce apoptosis in wild-type cells and cells from eitherbax−/− or bak−/− animals. In contrast, constitutively active forms of Bim and Bad failed to induce apoptosis in bax−/−bak−/− cells. Expression of Bax restored susceptibility of the cells to Bim and Bad. In addition, Bax but not Bim or Bad sensitized thebax−/−bak−/− cells to a wide variety of cell death stimuli including UV irradiation, chemotherapeutic agents, and ER stress. These results suggest that neither activation of BH3-only proteins nor suppression of pro-survival Bcl-2 proteins is sufficient to kill cells in the absence of both Bax and Bak. Furthermore, whereas mouse embryo fibroblasts (MEF) expressing only Bax or Bak displayed resistance to transformation,bax−/−bak−/− MEF were nearly as prone to oncogenic transformation as p53−/− MEF. Thus, the function of either Bax or Bak appears required to initiate most forms of apoptosis and to suppress oncogenic transformation.
SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins
Authors: Schultz David C. , Ayyanathan Kasirajan , Negorev Dmitri , Maul Gerd G. , Rauscher Frank J.
Published: July 2002

Posttranslational modification of histones has emerged as a key regulatory signal in eukaryotic gene expression. Recent genetic and biochemical studies link H3-lysine 9 (H3-K9) methylation to HP1-mediated heterochromatin formation and gene silencing. However, the mechanisms that target and coordinate these activities to specific genes is poorly understood. Here we report that the KAP-1 corepressor for the KRAB-ZFP superfamily of transcriptional silencers binds to SETDB1, a novel SET domain protein with histone H3-K9-specific methyltransferase activity. Although acetylation and phosphorylation of the H3 N-terminal tail profoundly affect the efficiency of H3-K9 methylation by SETDB1, we found that methylation of H3-K4 does not affect SETDB1-mediated methylation of H3-K9. In vitro methylation of the N-terminal tail of histone H3 by SETDB1 is sufficient to enhance the binding of HP1 proteins, which requires both an intact chromodomain and chromoshadow domain. Indirect immunofluoresence staining of interphase nuclei localized SETDB1 predominantly in euchromatic regions that overlap with HP1 staining in nonpericentromeric regions of chromatin. Moreover, KAP-1, SETDB1, H3-MeK9, and HP1 are enriched at promoter sequences of a euchromatic gene silenced by the KRAB–KAP-1 repression system. Thus, KAP-1 is a molecular scaffold that is targeted by KRAB-ZFPs to specific loci and coordinates both histone methylation and the deposition of HP1 proteins to silence gene expression.
A Microsphere-Based Assay for Multiplexed Single Nucleotide Polymorphism Analysis Using Single Base Chain Extension
Authors: Chen Jingwen , Iannone Marie A. , Li May-Sung , Taylor J. David , Rivers Philip , Nelsen Anita J. , Slentz-Kesler Kimberly A. , Roses Allen , Weiner Michael P.
Published: July 2002

A rapid, high throughput readout for single-nucleotide polymorphism (SNP) analysis was developed employing single base chain extension and cytometric analysis of an array of fluorescent microspheres. An array of fluorescent microspheres was coupled with uniquely identifying sequences, termed complementary ZipCodes (cZipCodes), which allowed for multiplexing possibilities. For a given assay, querying a polymorphic base involved extending an oligonucleotide containing both a ZipCode and a SNP-specific sequence with a DNA polymerase and a pair of fluoresceinated dideoxynucleotides. To capture the reaction products for analysis, the ZipCode portion of the oligonucleotide was hybridized with its cZipCodes on the microsphere. Flow cytometry was used for microsphere decoding and SNP typing by detecting the fluorescein label captured on the microspheres. In addition to multiplexing capability, the ZipCode system allows multiple sets of SNPs to be analyzed by a limited set of cZipCode-attached microspheres. A standard set of non-cross reactive ZipCodes was established experimentally and the accuracy of the system was validated by comparison with genotypes determined by other technologies. From a total of 58 SNPs, 55 SNPs were successfully analyzed in the first pass using this assay format and all 181 genotypes across the 55 SNPs were correct. These data demonstrate that the microsphere-based single base chain extension (SBCE) method is a sensitive and reliable assay. It can be readily adapted to an automated, high-throughput genotyping system.

[Primer sequences used in this study are available as online supplementary materials at www.genome.org.]
Discovery of a Novel, Paternally Expressed Ubiquitin-specific Processing Protease Gene through Comparative Analysis of an Imprinted Region of Mouse Chromosome 7 and Human Chromosome 19q13.4
Authors: Kim Joomyeong , Noskov Vladimir N. , Lu Xiaochen , Bergmann Anne , Ren Xiaojia , Warth Tiffany , Richardson Paul , Kouprina Natalya , Stubbs Lisa
Published: July 2002

Using mouse BAC clones spanning an imprinted interval of proximal mouse chromosome 7 and the genomic sequence of the related interval of human chromosome 19q13.4, we have identified a novel mouse gene,Usp29 (ubiquitin-specific processing protease 29), near two known imprinted genes, Peg3 and Zim1. GeneUsp29 is located directly adjacent to Peg3 in a “head-to-head” orientation, and comprises exons distributed over a genomic distance of at least 400 kb. A similar human gene is also found in the homologous location in human chromosome 19q13.4. The mouseUsp29 gene is also imprinted and is transcribed mainly from the paternal allele with highest expression levels in adult brain, especially in the cerebral cortex and hippocampus, and in the forebrain, face, and limb buds of midgestation mouse embryos. Analysis of a full-length 7.6-kb cDNA clone revealed that Usp29 encodes an 869-amino-acid protein that displays significant homology with yeast and nematode ubiquitin carboxyl-terminal hydrolases. These data suggest that, like the candidate Angelman syndrome gene Ube3a(ubiquitin ligase), Usp29 may represent another imprinted gene involved in the ubiquitination pathway. This identification of a third imprinted gene, Usp29, from the Peg3/Zim1-region confirms the presence of a conserved imprinted domain spanning at least 500 kb in the proximal portion of mouse chromosome 7 (Mmu7).

[The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AF229257 andAF229438.]
An Ordered Comparative Map of the Cattle and Human Genomes
Authors: Band Mark R. , Larson Joshua H. , Rebeiz Mark , Green Cheryl A. , Heyen D. Wayne , Donovan Jena , Windish Ryan , Steining Chad , Mahyuddin Prapti , Womack James E. , Lewin Harris A.
Published: July 2002

A cattle–human whole-genome comparative map was constructed using parallel radiation hybrid (RH) mapping in conjunction with EST sequencing, database mining for unmapped cattle genes, and a predictive bioinformatics approach (COMPASS) for targeting specific homologous regions. A total of 768 genes were placed on the RH map in addition to 319 microsatellites used as anchor markers. Of these, 638 had human orthologs with mapping data, thus permitting construction of an ordered comparative map. The large number of ordered loci revealed ⋝ 105 conserved segments between the two genomes. The comparative map suggests that 41 translocation events, a minimum of 54 internal rearrangements, and repositioning of all but one centromere can account for the observed organizations of the cattle and human genomes. In addition, the COMPASS in silico mapping tool was shown to be 95% accurate in its ability to predict cattle chromosome location from random sequence data, demonstrating this tool to be valuable for efficient targeting of specific regions for detailed mapping. The comparative map generated will be a cornerstone for elucidating mammalian chromosome phylogeny and the identification of genes of agricultural importance.“Ought we, for instance, to begin by discussing each separate species—in virtue of some common element of their nature, and proceed from this as a basis for the consideration of them separately?” from Aristotle, On the Parts of Animals, 350 B.C.E.

[The sequence data described in this paper have been submitted to the GenBank data library under accession nos.AW244888-AW244897, AW261132-AW261195, AW266849-AW267161,AW289175-AW289430, AW428566-AW428607, AW621146, AW621147.]
Predicting Splice Variant from DNA Chip Expression Data
Authors: Hu Gang Ken , Madore Steven J , Moldover Brian , Jatkoe Tim , Balaban David , Thomas Jeffrey , Wang Yixin
Published: July 2002

Alternative splicing of premessenger RNA is an important layer of regulation in eukaryotic gene expression. Splice variation of a large number of genes has been implicated in various cell growth and differentiation processes. To measure tissue-specific splicing of genes on a large scale, we collected gene expression data from 11 rat tissues using a high-density oligonucleotide array representing 1600 rat genes. Expression of each gene on the chip is measured by 20 pairs of independent oligonucleotide probes. Two algorithms have been developed to normalize and compare the chip hybridization signals among different tissues at individual oligonucleotide probe level. Oligonucleotide probes (the perfect match [PM] probe of each probe pair), detecting potential tissue-specific splice variants, were identified by the algorithms. The identified candidate splice variants have been compared to the alternatively spliced transcripts predicted by an EST clustering program. In addition, 50% of the top candidates predicted by the algorithms were confirmed by RT-PCR experiment. The study indicates that oligonucleotide probe-based DNA chip assays provide a powerful approach to detect splice variants at genome scale.
A Complete Sequence of the T. tengcongensis Genome
Authors: Bao Qiyu , Tian Yuqing , Li Wei , Xu Zuyuan , Xuan Zhenyu , Hu Songnian , Dong Wei , Yang Jian , Chen Yanjiong , Xue Yanfen , Xu Yi , Lai Xiaoqin , Huang Li , Dong Xiuzhu , Ma Yanhe , Ling Lunjiang , Tan Huarong , Chen Runsheng , Wang Jian , Yu Jun , Yang Huanming
Published: July 2002

Thermoanaerobacter tengcongensis is a rod-shaped, gram-negative, anaerobic eubacterium that was isolated from a freshwater hot spring in Tengchong, China. Using a whole-genome-shotgun method, we sequenced its 2,689,445-bp genome from an isolate, MB4T (Genbank accession no. AE008691). The genome encodes 2588 predicted coding sequences (CDS). Among them, 1764 (68.2%) are classified according to homology to other documented proteins, and the rest, 824 CDS (31.8%), are functionally unknown. One of the interesting features of the T. tengcongensis genome is that 86.7% of its genes are encoded on the leading strand of DNA replication. Based on protein sequence similarity, the T. tengcongensis genome is most similar to that of Bacillus halodurans, a mesophilic eubacterium, among all fully sequenced prokaryotic genomes up to date. Computational analysis on genes involved in basic metabolic pathways supports the experimental discovery that T. tengcongensis metabolizes sugars as principal energy and carbon source and utilizes thiosulfate and element sulfur, but not sulfate, as electron acceptors. T. tengcongensis, as a gram-negative rod by empirical definitions (such as staining), shares many genes that are characteristics of gram-positive bacteria whereas it is missing molecular components unique to gram-negative bacteria. A strong correlation between the G + C content of tDNA and rDNA genes and the optimal growth temperature is found among the sequenced thermophiles. It is concluded that thermophiles are a biologically and phylogenetically divergent group of prokaryotes that have converged to sustain extreme environmental conditions over evolutionary timescale.

[Supplemental material is available online athttp://www.genome.org.]
Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting
Authors: Blanchette Mathieu , Tompa Martin
Published: July 2002

Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of orthologous regulatory regions from multiple species. It does so by identifying the best conserved motifs in those orthologous regions. We describe a computer algorithm designed specifically for this purpose, making use of the phylogenetic relationships among the sequences under study to make more accurate predictions. The program is guaranteed to report all sets of motifs with the lowest parsimony scores, calculated with respect to the phylogenetic tree relating the input species. We report the results of this algorithm on several data sets of interest. A large number of known functional binding sites are identified by our method, but we also find several highly conserved motifs for which no function is yet known.
Large-Scale Protein Annotation through Gene Ontology
Authors: Xie Hanqing , Wasserman Alon , Levine Zurit , Novik Amit , Grebinskiy Vladimir , Shoshan Avi , Mintz Liat
Published: July 2002

Recent progress in genomic sequencing, computational biology, and ontology development has presented an opportunity to investigate biological systems from a unique perspective, that is, examining genomes and transcriptomes through the multiple and hierarchical structure of Gene Ontology (GO). We report here our development of GO Engine, a computational platform for GO annotation, and analysis of the resultant GO annotations of human proteins. Protein annotation was centered on sequence homology with GO-annotated proteins and protein domain analysis. Text information analysis and a multiparameter cellular localization predictive tool were also used to increase the annotation accuracy, and to predict novel annotations. The majority of proteins corresponding to full-length mRNA in GenBank, and the majority of proteins in the NR database (nonredundant database of proteins) were annotated with one or more GO nodes in each of the three GO categories. The annotations of GenBank and SWISS-PROT proteins are available to the public at the GO Consortium web site.
Extreme Reduction of Chromosome-Specific α-Satellite Array Is Unusually Common in Human Chromosome 21
Authors: Lo Anthony W.I. , Liao Gregory C.-C. , Rocchi Mariano , Choo K.H. Andy
Published: July 2002

Human centromeres contain large arrays of α-satellite DNA that are thought to provide centromere function. The arrays show size and sequence variation, but the extent to which extremely low levels of this DNA can occur on normal centromeres is unclear. Using a set of chromosome-specific α-satellite probes for each of the human chromosomes, we performed interphase fluorescence in situ hybridization (FISH) in a population-screening study. Our results demonstrate that extreme reduction of chromosome-specific α satellite is unusually common in chromosome 21 (screened with the αRI probe), with a prevalence of 3.70%, compared to ≤0.12% for each of chromosomes 13 and 17, and 0% for the other chromosomes. No analphoid centromere was identified in >17,000 morphologically normal chromosomes studied. All of the low-alphoid centromeres are fully functional as indicated by their mitotic stability and binding to centromere proteins CENP-B, CENP-C, and CENP-E. Sensitive metaphase FISH analysis of the low-alphoid chromosome 21 centromeres established the presence of residual αRI as well as other non-αRI α-satellite DNA suggesting that centromere function may be provided by (1) the residual αRI DNA, (2) other non-αRI α-satellite sequences, (3) a combination of 1 and 2, or (4) an activated neocentromere DNA. The low-alphoid centromeres, in particular those of chromosome 21, should provide unique opportunities for the study of the evolution and the minimal DNA requirement of the human centromere.
Genomic Analysis of Caenorhabditis elegans Reveals Ancient Families of Retroviral-like Elements
Authors: Bowen Nathan J. , McDonald John F.
Published: July 2002

Retrotransposons are the most abundant and widespread class of eukaryotic transposable elements. The recent genome sequencing ofCaenorhabditis elegans has provided an unprecedented opportunity to analyze the evolutionary relationships among the entire complement of retrotransposons within a multicellular eukaryotic organism. In this article we report the results of an analysis of retroviral-like long terminal repeat retrotransposons in C. elegans that indicate that this class of elements may be even more abundant and divergent than previously expected. The unexpected presence, in C. elegans, of an element displaying a number of characteristics previously thought to be unique to vertebrate retroviruses suggests an ancient lineage for this important class of infectious agents.
d2_cluster: A Validated Method for Clustering EST and Full-Length cDNA Sequences
Authors: Burke John , Davison Dan , Hide Winston
Published: July 2002

Several efforts are under way to condense single-read expressed sequence tags (ESTs) and full-length transcript data on a large scale by means of clustering or assembly. One goal of these projects is the construction of gene indices where transcripts are partitioned into index classes (or clusters) such that they are put into the same index class if and only if they represent the same gene. Accurate gene indexing facilitates gene expression studies and inexpensive and early partial gene sequence discovery through the assembly of ESTs that are derived from genes that have yet to be positionally cloned or obtained directly through genomic sequencing. We describe d2_cluster, an agglomerative algorithm for rapidly and accurately partitioning transcript databases into index classes by clustering sequences according to minimal linkage or “transitive closure” rules. We then evaluate the relative efficiency of d2_cluster with respect to other clustering tools. UniGene is chosen for comparison because of its high quality and wide acceptance. It is shown that although d2_cluster and UniGene produce results that are between 83% and 90% identical, the joining rate of d2_cluster is between 8% and 20% greater than UniGene. Finally, we present the first published rigorous evaluation of under and over clustering (in other words, of type I and type II errors) of a sequence clustering algorithm, although the existence of highly identical gene paralogs means that care must be taken in the interpretation of the type II error. Upper bounds for these d2_cluster error rates are estimated at 0.4% and 0.8%, respectively. In other words, the sensitivity and selectivity of d2_cluster are estimated to be >99.6% and 99.2%.

[Supplementary material to this paper may be found online at www.genome.org and atwww.pangeasystems.com.]
Toward Real-World Sequencing by Microdevice Electrophoresis
Authors: Schmalzing Dieter , Tsao Norman , Koutny Lance , Chisholm Dan , Srivastava Alok , Adourian Aram , Linton Lauren , McEwan Paul , Matsudaira Paul , Ehrlich Daniel
Published: July 2002

We report results using a microdevice for DNA sequencing using samples from chromosome 17, obtained from the Whitehead Institute Center for Genome Research (WICGR) production line. The device had an effective separation distance of 11.5 cm and a lithographically defined injection width of 150 μm. The four-color raw data were processed, base-called by the sequencing software Trout, and compared to the corresponding ABI 377 sequence from WICGR. With a criteria of 99% accuracy, we achieved average continuous reads of 505 bases in 27 min with 3% linear polyacrylamide (LPA) at 150 V/cm, and 460 bases in 22 min with 4% LPA at 200 V/cm at a temperature of 45°C. In the best case, up to 565 bases could be base-called with the same accuracy in <25 min. In some instances, Trout allowed for accurate base-calling down to a resolutionRas low asR = 0.35. This may be due in part to the high signal-to-noise ratio of the microdevice. Unlike many results reported on capillary machines, no additional sample cleanup other than ethanol precipitation was required. In addition, DNA fragment biasing (i.e., discrimination against larger fragments) was reduced significantly through the unique sample injection mechanism of the microfabricated device. This led to increased signal strength for long fragments, which is of great importance for the high performance of the microdevice.
LeCPK1, a Calcium-Dependent Protein Kinase from Tomato. Plasma Membrane Targeting and Biochemical Characterization
Authors: Rutschmann Frank , Stalder Urs , Piotrowski Markus , Oecking Claudia , Schaller Andreas
Published: July 2002

The cDNA of LeCPK1, a calcium-dependent protein kinase, was cloned from tomato (Lycopersicon esculentum Mill.). LeCPK1 was expressed in Escherichia coli and purified from bacterial extracts. The recombinant protein was shown to be a functional protein kinase using a synthetic peptide as the substrate (syntide-2,K  m = 85 μm). Autophosphorylation of LeCPK1 was observed on threonine and serine residues, one of which was identified as serine-439. Kinase activity was shown to be Ca2+ dependent and required the C-terminal, calmodulin-like domain of LeCPK1. Two classes of high- and low-affinity Ca2+-binding sites were observed, exhibiting dissociation constants of 0.6 and 55 μm, respectively. LeCPK1 was found to phosphorylate the regulatory C-terminal domain of the plasma membrane H+-ATPase in vitro. A potential role in the regulation of proton pump activity is corroborated by the apparent colocalization of the plasma membrane H+-ATPase and LeCPK1 in vivo. Upon transient expression in suspension-cultured cells, a C-terminal fusion of LeCPK1 with the green fluorescent protein was targeted to the plasma membrane. Myristoylation of theLeCPK1 N terminus was found to be required for plasma membrane targeting.
An Arabidopsis Calcium-Dependent Protein Kinase Is Associated with the Endoplasmic Reticulum
Authors: Lu Sheen X. , Hrabak Estelle M.
Published: July 2002

Arabidopsis contains 34 genes that are predicted to encode calcium-dependent protein kinases (CDPKs). CDPK enzymatic activity previously has been detected in many locations in plant cells, including the cytosol, the cytoskeleton, and the membrane fraction. However, little is known about the subcellular locations of individual CDPKs or the mechanisms involved in targeting them to those locations. We investigated the subcellular location of one Arabidopsis CDPK, AtCPK2, in detail. Membrane-associated AtCPK2 did not partition with the plasma membrane in a two-phase system. Sucrose gradient fractionation of microsomes demonstrated that AtCPK2 was associated with the endoplasmic reticulum (ER). AtCPK2 does not contain transmembrane domains or known ER-targeting signals, but does have predicted amino-terminal acylation sites. AtCPK2 was myristoylated in a cell-free extract and myristoylation was prevented by converting the glycine at the proposed site of myristate attachment to alanine (G2A). In plants, the G2A mutation decreased AtCPK2 membrane association by approximately 50%. A recombinant protein, consisting of the first 10 amino acids of AtCPK2 fused to the amino-terminus of β-glucuronidase, was also targeted to the ER, indicating that the amino terminus of AtCPK2 can specify ER localization of a soluble protein. These results indicate that AtCPK2 is localized to the ER, that myristoylation is likely to be involved in the membrane association of AtCPK2, and that the amino terminal region of AtCPK2 is sufficient for correct membrane targeting.
Mutational Analysis of the Ethylene Receptor ETR1. Role of the Histidine Kinase Domain in Dominant Ethylene Insensitivity
Authors: Gamble Rebekah L. , Qu Xiang , Schaller G. Eric
Published: July 2002

The ethylene receptor family of Arabidopsis consists of five members, one of these being ETR1. The N-terminal half of ETR1 contains a hydrophobic domain responsible for ethylene binding and membrane localization. The C-terminal half of the polypeptide contains domains with homology to histidine (His) kinases and response regulators, signaling motifs originally identified in bacteria. The role of the His kinase domain in ethylene signaling was examined in planta. For this purpose, site-directed mutations were introduced into the full-length wild-type ETR1 gene and into etr1-1, a mutant allele that confers dominant ethylene insensitivity on plants. The mutant forms of the receptor were expressed in Arabidopsis and the transgenic plants characterized for their ethylene responses. A mutation that eliminated His kinase activity did not affect the ability of etr1-1 to confer ethylene insensitivity. A truncated version of etr1-1 that lacks the His kinase domain also conferred ethylene insensitivity. Possible mechanisms by which a truncated version of etr1-1 could exert dominance are discussed.
Identification of an Arabidopsis thaliana Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Activase (RCA) Minimal Promoter Regulated by Light and the Circadian Clock
Authors: Liu Z. , Taub C. C. , McClung C. R.
Published: July 2002

Transcription of the Arabidopsis thaliana gene encoding ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) activase (RCA) is organ-specific, light-responsive, and regulated by the circadian clock. RCA is transcribed throughout the green parts of the plant, but not in roots and petals. Responses elicited by short pulses of light indicate that the light response is mediated, at least in part, by phytochrome. Analysis of transgenic tobacco and Arabidopsis carrying RCA 5[prime] untranscribed regions fused to reporter genes (uidA, encoding β-glucuronidase, or cat, encoding chloramphenicol acetyltransferase) indicate that elements sufficient to confer organ-specific, light-responsive, and clock-regulated transcription are localized within 317 base pairs upstream of the site of transcription initiation. A clock-responsive element sufficient to confer a low-amplitude (approximately 2-fold) circadian oscillation lies within 317 base pairs of the transcription start, but other elements necessary for high-amplitude (approximately 10-fold) circadian oscillation lie upstream of -317 and are removed by deletion from -970 to -317.
An Improved Green Fluorescent Protein Gene as a Vital Marker in Plants
Authors: Pang S. Z. , DeBoer D. L. , Wan Y. , Ye G. , Layton J. G. , Neher M. K. , Armstrong C. L. , Fry J. E. , Hinchee MAW. , Fromm M. E.
Published: July 2002

A synthetic green fluorescent protein (GFP) gene (pgfp) was constructed to improve GFP expression in plants. Corn and tobacco protoplast transient assays showed that pgfp gave about 20-fold brighter fluorescence than the wild-type gene (gfp). Replacement of the serine at position 65 with a threonine (S65Tpgfp) or a cysteine (S65Cpgfp) yielded 100- to 120-fold brighter fluorescence than wild-type gfp upon excitation with 490-nm light. Incorporation of a plant intron into the coding region yielded an additional 1.4-fold improvement, for a cumulative improvement of about 150-fold in fluorescence at 490-nm excitation. Various versions of pgfp were also stably introduced into corn, wheat, tobacco, and Arabidopsis plants. Bright-green fluorescence was observed with a fluorescence microscope in virtually all examined tissues of transgenic monocots and dicots. In the case of Arabidopsis, expression of the pgfp gene under the enhanced 35S promoter of the cauliflower mosaic virus produced green fluorescence that was readily detectable by eye using a hand-held, long-wave ultraviolet lamp and/or a black-light source.
Metabolic Bypass of the Tricarboxylic Acid Cycle during Lipid Mobilization in Germinating Oilseeds1
Authors: Falk Kimberly L. , Behal Robert H. , Xiang Chengbin , Oliver David J.
Published: July 2002

Biosynthesis of sucrose from triacylglycerol requires the bypass of the CO2-evolving reactions of the tricarboxylic acid (TCA) cycle. The regulation of the TCA cycle bypass during lipid mobilization was examined. Lipid mobilization in Brassica napus was initiated shortly after imbibition of the seed and proceeded until 2 d postimbibition, as measured by in vivo [1-14C]acetate feeding to whole seedlings. The activity of NAD+-isocitrate dehydrogenase (a decarboxylative enzyme) was not detected until 2 d postimbibition. RNA-blot analysis ofB. napus seedlings demonstrated that the mRNA for NAD+-isocitrate dehydrogenase was present in dry seeds and that its level increased through the 4 d of the experiment. This suggested that NAD+-isocitrate dehydrogenase activity was regulated by posttranscriptional mechanisms during early seedling development but was controlled by mRNA level after the 2nd or 3rd d. The activity of fumarase (a component of the nonbypassed section of the TCA cycle) was low but detectable in B. napus seedlings at 12 h postimbibition, coincident with germination, and increased for the next 4 d. RNA-blot analysis suggested that fumarase activity was regulated primarily by the level of its mRNA during germination and early seedling development. It is concluded that posttranscriptional regulation of NAD+-isocitrate dehydrogenase activity is one mechanism of restricting carbon flux through the decarboxylative section of the TCA cycle during lipid mobilization in germinating oilseeds.
The H+-Sucrose Cotransporter NtSUT1 Is Essential for Sugar Export from Tobacco Leaves1
Authors: Bürkle Lukas , Hibberd Julian M. , Quick W. Paul , Kühn Christina , Hirner Brigitte , Frommer Wolf B.
Published: July 2002

In many species translocation of sucrose from the mesophyll to the phloem is carrier mediated. A sucrose/H+-symporter cDNA,NtSUT1, was isolated from tobacco (Nicotiana tabacum) and shown to be highly expressed in mature leaves and at low levels in other tissues, including floral organs. To study the in vivo function of NtSUT1, tobacco plants were transformed with aSUT1 antisense construct under control of the cauliflower mosaic virus 35S promoter. Upon maturation, leaves of transformants expressing reduced amounts of SUT1 mRNA curled downward, and strongly affected plants developed chloroses and necroses that led to death. The leaves exhibited impaired ability to export recently fixed 14CO2 and were unable to export transient starch during extended periods of darkness. As a consequence, soluble carbohydrates accumulated and photosynthesis was reduced. Autoradiographs of leaves show a heterogenous pattern of CO2 fixation even after a 24-h chase. The 14C pattern does not change with time, suggesting that movement of photosynthate between mesophyll cells may also be impaired. The affected lines show a reduction in the development of the root system and delayed or impaired flowering. Taken together, the effects observed in a seed plant (tobacco) demonstrate the importance of SUT1 for sucrose loading into the phloem via an apoplastic route and possibly for intermesophyll transport as well.
Characterization of Transgenic Tobacco with an Increased α-Linolenic Acid Level
Authors: Hamada Tatsurou , Kodama Hiroaki , Takeshita Keizo , Utsumi Hideo , Iba Koh
Published: July 2002

Microsomal ω-3 fatty acid desaturase catalyzes the conversion of 18:2 (linoleic acid) to 18:3 (α-linolenic acid) in phospholipids, which are the main constituents of extrachloroplast membranes. Transgenic tobacco (Nicotiana tabacum) plants with increased 18:3 contents (designated SIIn plants) were produced through the introduction of a construct with the tobacco microsomal ω-3 fatty acid desaturase gene under the control of the highly efficient promoter containing the E12Ω sequence. 18:3 contents in the SIIn plants were increased by about 40% in roots and by about 10% in leaves compared with the control plants. With regard to growth at 15°C and 25°C and the ability to tolerate chilling at 1°C and 5°C, there were no discernible differences between the SIIn and the control plants. Freezing tolerance in leaves and roots, which was assessed by electrolyte leakage, was almost the same between the SIIn and the control plants. The fluidity of plasma membrane from the SIIn plants was almost the same as that of the control plants. These results indicate that an increase in the 18:3 level in phospholipids is not directly involved in compensation for the diminishment in growth or membrane properties observed under low temperatures.
Several Thaumatin-Like Proteins Bind to β-1,3-Glucans
Authors: Trudel Jean , Grenier Jean , Potvin Claude , Asselin Alain
Published: July 2002

Pathogenesis-related proteins from intercellular fluid washings of stressed barley (Hordeum vulgare L.) leaves were analyzed to determine their binding to various water-insoluble polysaccharides. Three proteins (19, 16, and 15 kD) bound specifically to several water-insoluble β-1,3-glucans. Binding of the barley proteins to pachyman occurred quickly at 22°C at pH 5.0, even in the presence of 0.5 m NaCl, 0.2m urea, and 1% (v/v) Triton X-100. Bound barley proteins were released by acidic treatments or by boiling in sodium dodecyl sulfate. Acid-released barley proteins could bind again specifically and singly to pachyman. Water-soluble laminarin and carboxymethyl-pachyman competed for the binding of the barley proteins to pachyman. The N-terminal sequence of the 19-kD barley β-1,3-glucan-binding protein showed near identity to the barley seed protein BP-R and high homology to other thaumatin-like (TL) permatins. The 16-kD barley protein was also homologous to TL proteins, whereas the 15-kD barley protein N-terminal sequence was identical to the pathogenesis-related Hv-1 TL protein. Antifungal barley protein BP-R and corn (Zea mays) zeamatin were isolated by binding to pachyman. Two extracellular proteins from stressed pea (Pisum sativum L.) also bound to pachyman and were homologous to TL proteins.