bluuebunny/crossref_metadata_2025_split huggingface dataset:
Host Factors That Affect Ty3 Retrotransposition in Saccharomyces cerevisiae
Authors: Aye Michael , Irwin Becky , Beliakova-Bethell Nadejda , Chen Eric , Garrus Jennifer , Sandmeyer Suzanne 
Published: December 2004

Abstract
The retrovirus-like element Ty3 of Saccharomyces cerevisiae integrates at the transcription initiation region of RNA polymerase III. To identify host genes that affect transposition, a collection of insertion mutants was screened using a genetic assay in which insertion of Ty3 activates expression of a tRNA suppressor. Fifty-three loci were identified in this screen. Corresponding knockout mutants were tested for the ability to mobilize a galactose-inducible Ty3, marked with the HIS3 gene. Of 42 mutants tested, 22 had phenotypes similar to those displayed in the original assay. The proteins encoded by the defective genes are involved in chromatin dynamics, transcription, RNA processing, protein modification, cell cycle regulation, nuclear import, and unknown functions. These mutants were induced for Ty3 expression and assayed for Gag3p protein, integrase, cDNA, and Ty3 integration upstream of chromosomal tDNAVal(AAC) genes. Most mutants displayed differences from the wild type in one or more intermediates, although these were typically not as severe as the genetic defect. Because a relatively large number of genes affecting retrotransposition can be identified in yeast and because the majority of these genes have mammalian homologs, this approach provides an avenue for the identification of potential antiviral targets.
Uncovering Novel Cell Cycle Players Through the Inactivation of Securin in Budding Yeast
Authors: Sarin Sumeet , Ross Karen E , Boucher Lorrie , Green Yvette , Tyers Mike , Cohen-Fix Orna 
Published: December 2004

Abstract
Budding yeast securin/Pds1p, an inhibitor of the anaphase activator separase/Esp1p, is involved in several checkpoint pathways and in promoting Esp1p's nuclear localization. Using a modified synthetic genetic array (SGA) screen for genes that become essential in the absence of Pds1p, we uncovered roles for uncharacterized genes in cell cycle processes, including Esp1p activation.
Phylogenetic Analysis of 5′-Noncoding Regions From the ABA-Responsive rab16/17 Gene Family of Sorghum, Maize and Rice Provides Insight Into the Composition, Organization and Function of cis-Regulatory ModulesSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession no. AY177889.
Authors: Buchanan Christina D , Klein Patricia E , Mullet John E 
Published: December 2004

Abstract
Phylogenetic analysis of sequences from gene families and homologous genes from species of varying divergence can be used to identify conserved noncoding regulatory elements. In this study, phylogenetic analysis of 5′-noncoding sequences was optimized using rab17, a well-characterized ABA-responsive gene from maize, and five additional rab16/17 homologs from sorghum and rice. Conserved 5′-noncoding sequences among the maize, sorghum, and rice rab16/17 homologs were identified with the aid of the software program FootPrinter and by screening for known transcription-factor-binding sites. Searches for 7 of 8 (7/8)bp sequence matches within aligned 5′-noncoding segments of the rab genes identified many of the cis-elements previously characterized by biochemical analysis in maize rab17 plus several additional putative regulatory elements. Differences in the composition of conserved noncoding sequences among rab16/17 genes were related to variation in rab gene mRNA levels in different tissues and to response to ABA treatment using qRT-PCR. Absence of a GRA-like element in the promoter of sorghum dhn2 relative to maize rab17 was correlated with an ∼85-fold reduction of dhn2 RNA in sorghum shoots. Overall, we conclude that phylogenetic analysis of gene families among rice, sorghum, and maize will help identify regulatory sequences in the noncoding regions of genes and contribute to our understanding of grass gene regulatory networks.
Insertion-Sequence-Mediated Mutations Isolated During Adaptation to Growth and Starvation in Lactococcus lactis
Authors: de Visser J Arjan G M , Akkermans Antoon D L , Hoekstra Rolf F , de Vos Willem M 
Published: December 2004

AbstractWe studied the activity of three multicopy insertion sequence (IS) elements in 12 populations of Lactococcus lactis IL1403 that evolved in the laboratory for 1000 generations under various environmental conditions (growth or starvation and shaken or stationary). Using RFLP analysis of single-clone representatives of each population, nine IS-mediated mutations were detected across all environmental conditions and all involving IS981. When it was assumed that these mutations were neutral, their frequency was higher under shaken than under stationary conditions, possibly due to oxygen stress. We characterized seven of the nine mutations at the molecular level and studied their population dynamics where possible. Two were simple insertions into new positions and the other five were recombinational deletions (of &lt;1–&gt;10 kb) among existing and new copies of IS981; in all but one case these mutations disrupted gene functions. The best candidate beneficial mutations were two deletions of which similar versions were detected in two populations each. One of these two parallel deletions, affecting a gene involved in bacteriophage resistance, showed intermediate rearrangements and may also have resulted from increased local transposition rates.
Subtelomeric 6p deletion: Clinical, FISH, and array CGH characterization of two cases
Authors: Le Caignec Cédric , De Mas Philippe , Vincent Marie‐Claire , Bocéno Michelle , Bourrouillou Georges , Rival Jean‐Marie , David Albert 
Published: December 2004

AbstractThirty patients have been described with cytogenetically visible deletion of the short arm of chromosome 6. However, subtelomeric 6p deletion detected by subtelomeric specific probes has been reported only twice. We report two new patients with terminal 6p deletion detected by subtelomeric screening using fluorescence in situ hybridization (FISH). The two patients exhibited mental retardation, ocular abnormalities, hearing loss, and a characteristic facial appearance. Detailed FISH analyses with probes covering the distal 6p25 region estimated the size of the terminal deletions to ≈5.5 Mb and ≈4.8 Mb. Array‐based comparative genomic hybridization (array CGH) was used to confirm the cryptic deletions. Most patients with subtelomeric defects lack a characteristic phenotype. However, some of the subtelomeric deletions result in a specific phenotype, which can direct the clinician towards the diagnosis. Submicroscopic 6p deletion appears to be a recognizable clinical phenotype, and this region should be thoroughly investigated with FISH probes, including at least a subtelomeric 6p probe and a probe covering FOXC1, for patients presenting with a characteristic facial appearance, ocular abnormalities, predominantly anterior‐chamber eye defects, hearing loss, and mental retardation. © 2004 Wiley‐Liss, Inc.
A clinical report of a patient with two abnormal cell lines: 46,XX,del(21)(q22.1) and 47,XX,+3
Authors: Quigley Denise I. , Sailus Jeffery , Kaiser‐Rogers Kathleen , Rao Kathleen W. , Calikoglu Muge , Gold Stuart , McCandless Shawn E. 
Published: December 2004

AbstractMosaicism for two chromosomally abnormal cell lines in the absence of a normal cell line is exceedingly rare. We report a patient with developmental and growth delay, mild dysmorphic features, a history of hypertension and hepatoblastoma who was found to be mosaic for two chromosomally abnormal cell lines. The cell lines, one containing a terminally deleted chromosome 21, the other trisomy 3, were found in her blood. Fibroblasts and hepatoblastoma tumor cells revealed only the presence of the deleted 21 cell line. Microsatellite marker analysis suggests a mosaic rather than chimeric etiology for the cell lines. This case is exceptional in that the presence of either of these two cell lines alone is uncommon; finding both of these cell lines in an individual appears to be unique. © 2004 Wiley‐Liss, Inc.
A locus for Bowen–Conradi syndrome maps to chromosome region 12p13.3
Authors: Lamont Ryan E. , Loredo‐Osti JC. , Roslin Nicole M. , Mauthe Jill , Coghlan Gail , Nylen Edward , Frappier Danielle , Innes A. Micheil , Lemire Edward G. , Lowry R. Brian , Greenberg Cheryl R. , Triggs‐Raine Barbara L. , Morgan Kenneth , Wrogemann Klaus , Fujiwara T. Mary , Zelinski Teresa 
Published: December 2004

AbstractBowen–Conradi syndrome (BCS) is a lethal autosomal recessive disorder with an estimated incidence of 1 in 355 live births in the Hutterite population. A few cases have been reported in other populations. Here, we report the results of a genome‐wide scan and fine mapping of the BCS locus in Hutterite families. By linkage and haplotype analysis the BCS locus was mapped to a 3.5 cM segment (1.9 Mbp) in chromosome region 12p13.3 bounded byF8VWFandD12S397. When genealogical relationships among the families were taken into account in the linkage analysis, the evidence for linkage was stronger and the number of potentially linked regions was reduced to one. Under the assumption that all the Hutterite patients were identical by descent for a disease‐causing mutation, haplotype analysis was used to infer likely historical recombinants and thereby narrow the candidate region to a chromosomal segment shared in common by all the affected children. This study also demonstrates that BCS and cerebro‐oculo‐facial‐skeletal syndrome (COFS) are genetically distinct. © 2004 Wiley‐Liss, Inc.
Endothelin‐mediated remodeling in aortas of diabetic rats
Authors: Fukuda Gen , Khan Zia A. , Barbin Yousef P. , Farhangkhoee Hana , Tilton Ronald G. , Chakrabarti Subrata 
Published: December 2004

AbstractBackgroundSmooth muscle cells proliferation and extracellular matrix (ECM) protein deposition are key features of diabetic macroangiopathy. In the present study, we have studied the role of endothelinA(ETA) receptor, the predominant receptor on smooth muscle cells, in diabetes‐induced vascular hypertrophy and remodeling.MethodsStreptozotocin‐induced diabetic rats were administrated a selective ETAreceptor antagonist, TBC3214, for 26 weeks. Following treatment, aortas were harvested and subjected to gene expression and morphometric analyses. We quantified fibronectin (FN) and plasminogen activator inhibitor‐1 (PAI‐1) expression as indicators of increased ECM protein synthesis. ET‐1, ET‐3, transforming growth factor‐β1 (TGF‐β1) and angiotensinogen mRNA levels were measured to elucidate genes involved in FN expression. We have investigated an embryonic splice variant of FN, oncofetal FN, and nonmuscle myosin heavy chain (SMemb) as vascular remodeling indicators.ResultsOur results show that diabetes leads to upregulation of FN, PAI‐1, ET‐1, ET‐3, TGF‐β1 and angiotensinogen mRNA levels in association with increased medial thickness. Immunohistochemical analyses revealed concurrent protein level changes. Diabetes also upregulated oncofetal FN and SMemb mRNA levels. Treatment with TBC3214 attenuated the mRNA levels of several genes and prevented increased medial thickness.ConclusionsThese results indicate that diabetes‐induced vascular hypertrophy and remodeling is associated with reexpression of embryonic forms of FN and myosin heavy chain. Such changes are ET‐dependent and may be mediated via TGF‐β1 and angiotensin. Copyright © 2004 John Wiley & Sons, Ltd.
Differential expression of tyrosinated tubulin in Spisula solidissima polar bodies
Authors: Alliegro Mark C. , Alliegro Mary Anne 
Published: December 2004

AbstractThe C‐terminus of α‐tubulin can be reversibly modified by a specific tyrosine ligase to yield an isoform known as Tyr‐tubulin. Tyr‐tubulin is typically found in more dynamic microtubule arrays such as the mitotic spindle, as opposed to stable structures like centrioles and flagella. In developing systems, it is expressed in relatively undifferentiated, proliferative cell types but is replaced by detyrosinated (Glu‐) tubulin during differentiation. We found Tyr‐tubulin highly enriched in a single polar body of Spisula solidissima embryos. Quantitation of DNA content by Hoechst staining indicates that polar body 1 (with twice the DNA content of polar body 2) is the Tyr‐tubulin–positive cell. Other than the apoptosis marker caspase, this is, to our knowledge, the first distinguishing marker antigen for polar bodies, particularly for one polar body vs. another. This localization of Tyr‐tubulin is unlikely to be a byproduct of the meiotic process itself, because it arises after ejection of both polar bodies is complete. Although polar bodies are typically thought of as a terminally differentiated vestige of meiosis, the localization of this more dynamic tubulin isoform suggests an active role in early development. Developmental Dynamics 232:216–220, 2005. © 2004 Wiley‐Liss, Inc.
Phenotypic analyses of mouse embryos with ubiquitous expression of Oct4: Effects on mid–hindbrain patterning and gene expression
Authors: Ramos‐Mejía Verónica , Escalante‐Alcalde Diana , Kunath Tilo , Ramírez Laura , Gertsenstein Marina , Nagy Andras , Lomelí Hilda 
Published: December 2004

AbstractOct4 is a transcription factor that has been associated with pluripotency and fate determination in the initial cell lineages of mammals. On the other hand, Pou2, the ortholog of Oct4 in zebrafish, serves additional later functions during brain development acting as a differentiation switch. In mice, Oct4 is expressed throughout the neural plate of embryos until embryonic day (E) 8.0. In this study, we produced transgenic mouse embryos that ubiquitously express Oct4 and analyzed the consequences during development. We show that, at E8.0, a higher dosage of Oct4 in the neuroectoderm is sufficient to transiently alter mid–hindbrain patterning and produced a strong up‐regulation of Pax2, indicating that Oct4 can regulate this gene in vivo. After E9.5, ectopic Oct4 in this region produced cell death and affected the development of the forebrain, suggesting that, at these later stages, Oct4 down‐regulation is necessary for normal development to proceed. The phenotype of the transgenic embryos was also accompanied with an increase of Fgf8 expression in several of its endogenous domains, suggesting the possibility that Oct4 can participate in the regulation of expression of this ligand. Our observations support the hypothesis that Oct4, like zebrafish Pou2, has a conserved function during early brain patterning in mouse. Developmental Dynamics 232:180–190, 2005. © 2004 Wiley‐Liss, Inc.
Mph2 expression in germinal zones of the mouse brain
Authors: Kim Mary H. , Gunnersen Jenny M. , Tan Seong‐Seng 
Published: December 2004

AbstractThe telencephalon develops from a seemingly homogeneous population of precursor cells that generates neurons with divergent properties and cell fates. An important question concerns the genetic control of cell states belonging to different generations. Mph2 was identified by serial analysis of gene expression as a differentially expressed gene during cortical development. Belonging to the Polycomb group, Mph2 may be involved in transcriptional repression of cell states from one generation to the next. Here, we use in situ hybridization to determine the spatial localization of Mph2 expression in the developing nervous system. Mph2 expression evident in proliferating precursor cell populations in the developing mouse brain such as the ventricular zones of the cortex and ganglionic eminences as well as in mature structures such as the granule cell layer of the adult dentate gyrus and cerebellum indicates a role for Mph2 in both the developing and adult brain. Developmental Dynamics 232:209–215, 2005. © 2004 Wiley‐Liss, Inc.
Transduction of naive CD4 T cells with kinase‐deficient Lck‐HIV‐Tat fusion protein dampens T cell activation and provokes a switch to regulatory function
Authors: Veldhoen Marc , Magee Anthony I. , Penha‐Goncalves Mario N. , Stockinger Brigitta 
Published: December 2004

AbstractWe show here that T cell differentiation can be altered by exposing naive mouse CD4 T cells to altered T cell receptor signaling, achieved by transducing them with a fusion protein consisting of a modified Lck protein lacking the kinase domain and the HIV‐Tat protein transduction domain. The Lck‐HIV‐Tat fusion protein is internalized into naive mouse T cells within 30 min after application to the medium. Activation of transduced cells in vitro resulted in strongly reduced intracellular calcium mobilization, alterations in cytokine profile, and sustained up‐regulation of CD25. The cells had suppressive activity in vitro, but no Foxp3 expression. Our data indicate that signals encountered by a naive T cell during its initial activation can profoundly influence its subsequent functional behavior and elicit T cells, which can have regulatory activity.
Value at risk from econometric models and implied from currency options
Authors: Chong James 
Published: December 2004

AbstractThis paper compares daily exchange rate value at risk estimates derived from econometric models with those implied by the prices of traded options. Univariate and multivariate GARCH models are employed in parallel with the simple historical and exponentially weighted moving average methods. Overall, we find that during periods of stability, the implied model tends to overestimate value at risk, hence over‐allocating capital. However, during turbulent periods, it is less responsive than the GARCH‐type models, resulting in an under‐allocation of capital and a greater number of failures. Hence our main conclusion, which has important implications for risk management, is that market expectations of future volatility and correlation, as determined from the prices of traded options, may not be optimal tools for determining value at risk. Therefore, alternative models for estimating volatility should be sought. Copyright © 2004 John Wiley & Sons, Ltd.
Profiling histidine‐containing dipeptides in rat tissues by liquid chromatography/electrospray ionization tandem mass spectrometry
Authors: Aldini Giancarlo , Orioli Marica , Carini Marina , Maffei Facino Roberto 
Published: December 2004

AbstractThe histidine‐containing dipeptides carnosine (CAR) and structurally related anserine (ANS) and homocarnosine (HCAR), widely distributed in vertebrate organisms, have recently been proposed as endogenous quenchers for highly cytotoxic α,β‐unsaturated aldehydes generated by peroxidation. A sensitive, selective, specific and rapid liquid chromatographic/electrospray ionization tandem mass spectrometric assay was developed and validated for the simultaneous determination of these peptides in biological matrices in order to establish their plasma/tissue distribution. Samples (plasma or tissue homogenates from male rats) were prepared by protein precipitation with HClO4 (1 : 1, v/v) containing H‐Tyr‐His‐OH as internal standard. The supernatant was separated on a Phenomenex Sinergy polar‐RP column with a mobile phase of water–acetonitrile–heptafluorobutyric acid (9 : 1 : 0.01, v/v/v) at a flow‐rate of 0.2 ml min−1, with a run time of 10 min. Detection was effected on an ion trap mass spectrometer equipped with an electrospray ionization interface operating in positive ionization mode. The acquisitions were in the multiple reaction monitoring mode using the following precursor → product ion combinations: H‐Tyr‐His‐OH (internal standard) m/z 319 → 301; CAR m/z 227 → 210 + 209; ANS m/z 241 → 224 + 197 + 170; HCAR m/z 241 → 156. The method was validated over the concentration range 15–1000 nmol g−1 and the limit of quantification (LOQ) and limit of detection (LOD) were 12.5 and 4.2 pmol injected, respectively. The intra‐ and inter‐day precisions were <10% (≤17.47% at the LOQ) and the intra‐ and inter‐assay accuracies were within ±10% for all concentrations. The mapping profile in rat tissue gave the following results: the highest concentrations of CAR and ANS were found in skeletal muscles (soleus, gastrocnemius, tibialis), followed by the heart, cerebellum and brain (ANS below the LOQ). HCAR was found only in the brain and cerebellum. No histidine‐containing dipeptides were detectable in plasma, liver, kidney and lung. Copyright © 2004 John Wiley & Sons, Ltd.
Identification of proteins by combination of size‐exclusion chromatography with matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry and comparison of some desalting procedures for both intact proteins and their tryptic digests
Authors: Šalplachta Jiří , Řehulka Pavel , Chmelík Josef 
Published: December 2004

AbstractSeparation of a protein mixture by size‐exclusion chromatography (SEC) was combined with matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS). Identification of proteins in the collected fractions was performed both as intact proteins by MALDI‐TOFMS and using peptide mass fingerprinting (PMF) after their digestion with trypsin. The presence of salts mostly disturbs the MALDI‐TOFMS signal and, therefore, proper purification or desalting procedures must be employed. Four desalting procedures (desalting column packed with Sephadex G‐100, on‐target washing, centrifugal filter devices and ZipTip C18) for purification of fractions of proteins separated by SEC and their tryptic digests prior to determination of their exact molecular masses by MALDI‐TOFMS were compared. In the case of intact proteins, the experiments showed that the best desalting procedures are the use of ZipTip C18 pipette tips and Ultrafree CL centrifugal filter devices. The peptide digests can be purified by using ZipTip C18 pipette tips or on‐target washing when both of these procedures provide similar results. On‐target washing can be used as a simple procedure to improve the mass spectra of salt‐containing samples. Analyses of the droplets collected after the on‐target washing show losses of sample and matrix caused by dissolution of these compounds during this procedure. Further, it was found that protein identification based on PMF is more sensitive than analyses of intact proteins and that multiple on‐target washing is very advantageous for analyses of peptide mixtures with a high content of salts. Copyright © 2004 John Wiley & Sons, Ltd.