bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deletions within a CA-repeat-rich region of intron 4 of the human SP-B gene affect mRNA splicing
Authors: Lin Zhenwu , Thomas Neal J. , Wang Yunhua , Guo Xiaoxuan , Seifart Carola , Shakoor Hasan , Floros Joanna 
Published: July 2005

Length variants within a CA-repeat-rich region of intron 4 of the human SP-B (pulmonary surfactant protein-B) gene are associated with several lung diseases. The hypothesis that SP-B intron 4 affects mRNA splicing was studied. SP-B minigenes containing exons 1–6 with a normal-sized intron 4 (pBi4normal) or intron 4 containing deletions (pBi4del) of 193, 211, 264 or 340 bp were expressed in CHO (Chinese hamster ovary) cells by transient transfection. Two forms of SP-B transcripts, normal and incompletely spliced, were detected. With pBi4normal, normal-sized SP-B mRNA was the predominant form and a very low amount of incompletely spliced mRNA was present, whereas with the pBi4del variants the amount of normal SP-B mRNAs was lower and the amount of incompletely spliced mRNA was relatively high. Reverse transcription–PCR results and sequencing data indicated that the incompletely spliced SP-B RNA contained intron 4 sequence, and this incompletely spliced RNA was also observed in normal lung. Lung cancer tissues with intron 4 deletions exhibited a larger amount of abnormally spliced RNAs compared with normal lung tissue or cancerous tissue with normal-sized intron 4. The results indicate that intron 4 length variants affect SP-B mRNA splicing, and that this may contribute to lung disease.
Thiol–disulphide interchange in tubulin: kinetics and the effect on polymerization
Authors: Britto P. J. , Knipling Leslie , Mcphie Peter , Wolff J. 
Published: July 2005

All 20 cysteine residues are accessible to disulphide reagents in the tubulin dimer, whereas only four are accessible in taxol-stabilized microtubules. Reaction rates with disulphide reagents are a function of the reagent, are decreased by G nucleotides, and increased with increase in pH and urea. With transient (stop-flow) kinetics, DTNB [5,5′-dithiobis-(2-nitrobenzoic acid)] and 2,2′-dithiodipyridine progress curves cannot be fitted by the sum of exponential terms based only on classes of cysteines. The mixed disulphide products react further to form both intra- and intermonomer disulphide bonds that can be reversed by reducing agents. With MMTS (methyl methanethiosulphonate) or ODNB (n-octyl-dithio-2-nitrobenzoate), virtually no protein–protein disulphide bonds are formed and the ODNB reaction can be given as the sum of three exponential terms with pseudo-first-order rate constants of 0.206, 0.069 and 0.010 s−1 at pH 6.5, suggesting three classes of thiol reactivities. Limited cysteine substitution leads to only small changes in tryptophan or CD spectra, whereas complete substitution leads to loss of the helix content. MMTS-induced loss of SH groups leads to progressive increases in the critical concentration and loss of polymerization competence that can be reversed by assembly promoters such as higher protein concentration, taxol or high ionic strength. Under such conditions, the substituted tubulin forms protofilament-based structures such as microtubules, open tubules, sheets and/or bundles.
Up-regulation of phospholipid hydroperoxide glutathione peroxidase in rat casein-induced polymorphonuclear neutrophils
Authors: Hattori Hiroyuki , Imai Hirotaka , Hanamoto Akiharu , Furuhama Kazuhisa , Nakagawa Yasuhito 
Published: July 2005

Antioxidant enzymes play key roles in the protection of cells from oxidative damage. Little is known, however, about the expression of antioxidants and/or their roles in PMNs (polymorphonuclear leucocytes), which are thought to suffer from oxidative stress in an inflammation site. In the present paper, we report on the regulation of expression of PHGPx (phospholipid hydroperoxide glutathione peroxidase) and cGPx (cytosolic glutathione peroxidase) in rat PMNs in the inflammation site. PHGPx mRNA levels were much lower in casein-induced peritoneal and carrageenan-induced pleural PMNs just after their collection than in peripheral PMNs. cGPx mRNA was also reduced in the casein-induced PMNs, but not in carrageenan-induced PMNs. Both enzymes with decreased levels in the casein-induced PMNs were up-regulated during further 24 h cultivation in vitro and in vivo, with elevation of their protein levels and activities, and reduction of intracellular peroxides. Up-regulation of PHGPx mRNA was attenuated by cycloheximide, a protein synthesis inhibitor, and this effect was cancelled by culturing the cells in the conditioned medium of the cultured casein-induced PMNs. This latter effect was attenuated by pre-treatment with anti-GRO (growth-regulated oncogene) antibody. Recombinant rat GRO could also induce the up-regulation in the presence of cycloheximide, demonstrating that GRO may play an important role in the PHGPx up-regulation of casein-induced PMNs. Production of the lipid mediators leukotriene B4 and 5-HETE (5-hydroxyeicosatetraenoic acid) was decreased in the cultured casein-induced PMNs exhibiting PHGPx up-regulation. The evidence obtained indicates that PHGPx activity in the activated PMNs would be related to the appearance of the intrinsic function of PMNs in the inflammatory site.
Structural basis for the interaction between human milk oligosaccharides and the bacterial lectin PA-IIL of Pseudomonas aeruginosa
Authors: Perret Stéphanie , Sabin Charles , Dumon Claire , Pokorná Martina , Gautier Catherine , Galanina Oxana , Ilia Shahov , Bovin Nicolai , Nicaise Magali , Desmadril Michel , Gilboa-Garber Nechama , Wimmerov´ Michaela , Mitchell Edward P. , Imberty Anne 
Published: July 2005

One of the mechanisms contributing to the protection by breast-feeding of the newborn against enteric diseases is related to the ability of human milk oligosaccharides to prevent the attachment of pathogenic bacteria to the duodenual epithelium. Indeed, a variety of fucosylated oligosaccharides, specific to human milk, form part of the innate immune system. In the present study, we demonstrate the specific blocking of PA-IIL, a fucose-binding lectin of the human pathogen Pseudomonas aeruginosa, by milk oligosaccharides. Two fucosylated epitopes, Lewis a and 3-fucosyl-lactose (Lewis x glucose analogue) bind to the lectin with dissociation constants of 2.2×10−7 M and 3.6×10−7 M respectively. Thermodynamic studies indicate that these interactions are dominated by enthalpy. The entropy contribution is slightly favourable when binding to fucose and to the highest-affinity ligand, Lewis a. The high-resolution X-ray structures of two complexes of PA-IIL with milk oligosaccharides allow the precise determination of the conformation of a trisaccharide and a pentasaccharide. The different types of interaction between the oligosaccharides and the protein involve not only hydrogen bonding, but also calcium- and water-bridged contacts, allowing a rationalization of the thermodynamic data. This study provides important structural information about compounds that could be of general application in new therapeutic strategies against bacterial infections.
In vivo characterization of the first acyl-CoA Δ6-desaturase from a member of the plant kingdom, the microalga Ostreococcus tauri
Authors: Domergue Frédéric , Abbadi Amine , Zähringer Ulrich , Moreau Hervé , Heinz Ernst 
Published: July 2005

Genomic DNA of Ostreococcus tauri, a fully sequenced marine unicellular alga from the phytoplankton, was used to amplify a gene coding for a typical front-end desaturase involved in polyunsaturated fatty acid biosynthesis. Heterologous expression in Saccharomyces cerevisiae revealed very high desaturation activity with Δ6-regioselectivity. Short-time kinetic experiments showed that the desaturase product was detected in the acyl-CoA pool 5 min after addition of the exogenous substrate to the yeast medium and long before its appearance in the total fatty acids. When this desaturase was co-expressed with the acyl-CoA Δ6-elongase from Physcomitrella patens and the lipid-linked Δ5-desaturase from Phaeodactylum tricornutum, high proportions of arachidonic or eicosapentaenoic acid were obtained, because nearly all of the Δ6-desaturated products were elongated. Furthermore, the product/educt ratios calculated in each glycerolipid for the Δ6-desaturase or for the acyl-CoA Δ6-elongase were in about the same range, whereas this ratio showed a very uneven profile in the case of the lipid-linked Δ5-desaturase. Finally, a sequence-based comparison of all the functionally characterized Δ6-desaturases showed that this enzyme was not related to any previously described sequence. Altogether, our data suggest that this desaturase from O. tauri is an acyl-CoA Δ6-desaturase, the first one cloned from a photosynthetically active organism.
The CB1 receptor antagonist rimonabant reverses the diet‐induced obesity phenotype through the regulation of lipolysis and energy balance
Authors: Jbilo Omar , Ravinet‐Trillou Christine , Arnone Michèle , Buisson Isabelle , Bribes Estelle , Péleraux Annick , Pénarier Géraldine , Soubrié Philippe , Le Fur Gérard , Galiègue Sylvaine , Casellas Pierre 
Published: July 2005

ABSTRACTWe investigated the molecular events involved in the long‐lasting reduction of adipose mass by the selective CB1 antagonist, SR141716. Its effects were assessed at the transcriptional level both in white (WAT) and brown (BAT) adipose tissues in a diet‐induced obesity model in mice. Our data clearly indicated that SR141716 reversed the phenotype of obese adipocytes at both macroscopic and genomic levels. First, oral treatment with SR141716 at 10 mg/kg/d for 40 days induced a robust reduction of obesity, as shown by the 50% decrease in adipose mass together with a major restoration of white adipocyte morphology similar to lean animals. Second, we found that the major alterations in gene expression levels induced by obesity in WAT and BAT were mostly reversed in SR141716‐treated obese mice. Importantly, the transcriptional patterns of treated obese mice were similar to those obtained in the CB1 receptor knockout mice fed a high‐fat regimen and which are resistant to obesity, supporting a CB1 receptor‐mediated process. Functional analysis of these modulations indicated that the reduction of adipose mass by the molecule resulted from an enhanced lipolysis through the induction of enzymes of the β‐oxidation and TCA cycle, increased energy expenditure, mainly through futile cycling (calcium and substrate), and a tight regulation of glucose homeostasis. These changes accompanied a significant cellular remodeling and contributed to a reduction of the obesity‐related inflammatory status. In addition to a transient reduction of food consumption, increases of both fatty acid oxidation and energy expenditure induced by the molecule summate leading to a sustained weight loss. Altogether, these data strongly indicate that the endocannabinoid system has a major role in the regulation of energy metabolism.
Mechanism of the defect in gap‐junctional communication by expression of a connexin 26 mutant associated with dominant deafness
Authors: Chen Yongyue , Deng Yanqin , Bao Xiaoyong , Reuss Luis , Altenberg Guillermo A. 
Published: July 2005

ABSTRACTGap‐junctional channels (connexin oligomers) are large‐diameter aqueous pores formed by head‐to‐head association of two gap‐junctional hemichannels, one from each of the adjacent cells. Profound hearing loss of genetic origin is common, and mutations of connexin 26 (Cx26) are the most frequent cause of this disorder. The Cx26 R75W mutant has been associated with disruption of cell‐to‐cell communication and profound hearing loss, but the mechanism of the gap‐junctional defect is unknown. Here, we show that Cx26 R75W forms gap‐junctional hemichannels that display altered voltage dependency and reduced permeability, and which cannot form functional gap‐junctional channels between neighboring cells. The R75W phenotype is dominant at the gap‐junction channel but not at the hemichannel level. Therefore, the absence of gap‐junctional communication caused by R75W expression is due to defective gap‐junction formation by functional hemichannels.
Novel drug development opportunity for relaxin in acute myocardial infarction: evidences from a swine model
Authors: Perna Avio‐Maria , Masini Emanuela , Nistri Silvia , Briganti Vittorio , Chiappini Laura , Stefano Pierluigi , Bigazzi Mario , Pieroni Cesco , Sacchi Tatiana Bani , Bani Daniele 
Published: July 2005

ABSTRACTThe hormone relaxin has been shown to cause coronary vasodilation and to prevent ischemia/reperfusion‐induced cardiac injury in rodents. This study provides evidence that relaxin, used as an adjunctive drug to coronary reperfusion, reduces the functional, biochemical, and histopathological signs of myocardial injury in an in vivo swine model of heart ischemia/reperfusion, currently used to test cardiotropic drugs for myocardial infarction. Human recombinant relaxin, given at reperfusion at doses of 1.25, 2.5, and 5 µg/kg b.wt. after a 30‐min ischemia, caused a dose‐related reduction of key markers of myocardial damage (serum myoglobin, CK‐MB, troponin T) and cardiomyocyte apoptosis (caspase 3, TUNEL assay), as well as of cardiomyocyte contractile dysfunction (myofibril hypercontraction). Compared with the controls, relaxin also increased the uptake of the viability tracer 201Thallium and improved ventricular performance (cardiac index). Relaxin likely acts by reducing oxygen free radical‐induced myocardial injury (malondialdehyde, tissue calcium overload) and inflammatory leukocyte recruitment (myeloperoxidase). The present findings show that human relaxin, given as a drug to counteract reperfusion‐induced cardiac injury, affords a clear‐cut protection to the heart of swine with induced myocardial infarction. The findings also provide background to future clinical trials with relaxin as adjunctive therapy to catheter‐based coronary angioplasty in patients with acute myocardial infarction.
Engineering Cytoplasmic Male Sterility via the Chloroplast Genome by Expression of β-Ketothiolase
Authors: Ruiz Oscar N. , Daniell Henry 
Published: July 2005

Abstract
While investigating expression of the polydroxybutyrate pathway in transgenic chloroplasts, we addressed the specific role of β-ketothiolase. Therefore, we expressed the phaA gene via the chloroplast genome. Prior attempts to express the phaA gene in transgenic plants were unsuccessful. We studied the effect of light regulation of the phaA gene using the psbA promoter and 5′ untranslated region, and evaluated expression under different photoperiods. Stable transgene integration into the chloroplast genome and homoplasmy were confirmed by Southern analysis. The phaA gene was efficiently transcribed in all tissue types examined, including leaves, flowers, and anthers. Coomassie-stained gel and western blots confirmed hyperexpression of β-ketothiolase in leaves and anthers, with proportionately high levels of enzyme activity. The transgenic lines were normal except for the male-sterile phenotype, lacking pollen. Scanning electron microscopy revealed a collapsed morphology of the pollen grains. Floral developmental studies revealed that transgenic lines showed an accelerated pattern of anther development, affecting their maturation, and resulted in aberrant tissue patterns. Abnormal thickening of the outer wall, enlarged endothecium, and vacuolation affected pollen grains and resulted in the irregular shape or collapsed phenotype. Reversibility of the male-sterile phenotype was observed under continuous illumination, resulting in viable pollen and copious amount of seeds. This study results in the first engineered cytoplasmic male-sterility system in plants, offers a new tool for transgene containment for both nuclear and organelle genomes, and provides an expedient mechanism for F1 hybrid seed production.
Complex Organization and Evolution of the Tomato Pericentromeric Region at the FER Gene Locus
Authors: Guyot Romain , Cheng Xudong , Su Yan , Cheng Zhukuan , Schlagenhauf Edith , Keller Beat , Ling Hong-Qing 
Published: July 2005

Abstract
Tomato (Lycopersicon esculentum) is a model species for molecular biology research and a candidate for large-scale genome sequencing. Pericentromeric heterochromatin constitutes a large portion of the tomato chromosomes. However, the knowledge of the structure, organization, and evolution of such regions remains very limited. Here, we report the analysis of a 198-kb sequence near the FER gene, located in a distal part of pericentromeric heterochromatin on the long arm of tomato chromosome 6. Nine genes, one pseudogene, and 55 transposable elements (TEs) were identified, showing a low gene density (19.8 kb/gene) and a high content of transposable elements (&gt;45% of the sequence). Six genes (56B23_g3, g5, g7, g8, g9, and g10) have perfect matches (&gt;98% identity) with tomato expressed sequence tags. Two genes (56B23_g1 and g6), which share &lt;98% sequence identity with expressed sequence tags, were confirmed for transcriptional activity by reverse transcription-PCR. The genes were not uniformly distributed along the sequence and grouped into gene islands separated by stretches of retrotransposons, forming a pattern similar to that found in the gene-rich regions of the large genomes of maize (Zea mays) and Triticeae. Long terminal repeat retrotransposons account for 60% of the TE sequence length. Sixteen of 55 TEs were completely new and remain unclassified. Surprisingly, five of the seven identified DNA transposons were closely associated with coding regions. The action of transposable elements and DNA rearrangements form the molecular basis of the dynamic genome evolution at the FER locus. Multiple rounds of genome duplication in Arabidopsis (Arabidopsis thaliana) and subsequent gene loss have generated a mosaic pattern of conservation between tomato and Arabidopsis orthologous sequences. Our data show that the distal parts of pericentromeric heterochromatin may contain many valuable genes and that these regions form an evolutionary active part of the tomato genome.
It's All GO for Plant Scientists
Authors: Clark Jennifer I. , Brooksbank Cath , Lomax Jane 
Published: July 2005

Abstract
The Gene Ontology project (http://www.geneontology.org/) produces structured, controlled vocabularies and gene product annotations. Gene products are classified according to the cellular locations and biological process in which they act, and the molecular functions that they carry out. We annotate gene products from a broad range of model species and provide support for those groups that wish to contribute annotation of further model species. The Gene Ontology facilitates the exchange of information between groups of scientists studying similar processes in different model organisms, and so provides a broad range of opportunities for plant scientists.
Plant Genome Resources at the National Center for Biotechnology Information
Authors: Wheeler David L. , Smith-White Brian , Chetvernin Vyacheslav , Resenchuk Sergei , Dombrowski Susan M. , Pechous Steven W. , Tatusova Tatiana , Ostell James 
Published: July 2005

Abstract
The National Center for Biotechnology Information (NCBI) integrates data from more than 20 biological databases through a flexible search and retrieval system called Entrez. A core Entrez database, Entrez Nucleotide, includes GenBank and is tightly linked to the NCBI Taxonomy database, the Entrez Protein database, and the scientific literature in PubMed. A suite of more specialized databases for genomes, genes, gene families, gene expression, gene variation, and protein domains dovetails with the core databases to make Entrez a powerful system for genomic research. Linked to the full range of Entrez databases is the NCBI Map Viewer, which displays aligned genetic, physical, and sequence maps for eukaryotic genomes including those of many plants. A specialized plant query page allow maps from all plant genomes covered by the Map Viewer to be searched in tandem to produce a display of aligned maps from several species. PlantBLAST searches against the sequences shown in the Map Viewer allow BLAST alignments to be viewed within a genomic context. In addition, precomputed sequence similarities, such as those for proteins offered by BLAST Link, enable fluid navigation from unannotated to annotated sequences, quickening the pace of discovery. NCBI Web pages for plants, such as Plant Genome Central, complete the system by providing centralized access to NCBI's genomic resources as well as links to organism-specific Web pages beyond NCBI.
Extension of the Visualization Tool MapMan to Allow Statistical Analysis of Arrays, Display of Coresponding Genes, and Comparison with Known Responses
Authors: Usadel Björn , Nagel Axel , Thimm Oliver , Redestig Henning , Blaesing Oliver E. , Palacios-Rojas Natalia , Selbig Joachim , Hannemann Jan , Piques Maria Conceição , Steinhauser Dirk , Scheible Wolf-Rüdiger , Gibon Yves , Morcuende Rosa , Weicht Daniel , Meyer Svenja , Stitt Mark 
Published: July 2005

Abstract
MapMan is a user-driven tool that displays large genomics datasets onto diagrams of metabolic pathways or other processes. Here, we present new developments, including improvements of the gene assignments and the user interface, a strategy to visualize multilayered datasets, the incorporation of statistics packages, and extensions of the software to incorporate more biological information including visualization of coresponding genes and horizontal searches for similar global responses across large numbers of arrays.
KaPPA-View. A Web-Based Analysis Tool for Integration of Transcript and Metabolite Data on Plant Metabolic Pathway Maps
Authors: Tokimatsu Toshiaki , Sakurai Nozomu , Suzuki Hideyuki , Ohta Hiroyuki , Nishitani Kazuhiko , Koyama Tanetoshi , Umezawa Toshiaki , Misawa Norihiko , Saito Kazuki , Shibata Daisuke 
Published: July 2005

Abstract
The application of DNA array technology and chromatographic separation techniques coupled with mass spectrometry to transcriptomic and metabolomic analyses in plants has resulted in the generation of considerable quantitative data related to transcription and metabolism. The integration of “omic” data is one of the major concerns associated with research into identifying gene function. Thus, we developed a Web-based tool, KaPPA-View, for representing quantitative data for individual transcripts and/or metabolites on plant metabolic pathway maps. We prepared a set of comprehensive metabolic pathway maps for Arabidopsis (Arabidopsis thaliana) and depicted these graphically in Scalable Vector Graphics format. Individual transcripts assigned to a reaction are represented symbolically together with the symbols of the reaction and metabolites on metabolic pathway maps. Using quantitative values for transcripts and/or metabolites submitted by the user as Comma Separated Value-formatted text through the Internet, the KaPPA-View server inserts colored symbols corresponding to a defined metabolic process at that site on the maps and returns them to the user's browser. The server also provides information on transcripts and metabolites in pop-up windows. To demonstrate the process, we describe the dataset obtained for transgenic plants that overexpress the PAP1 gene encoding a MYB transcription factor on metabolic pathway maps. The presentation of data in this manner is useful for viewing metabolic data in a way that facilitates the discussion of gene function.