bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nucleolus: Structure and Function
Authors: Olson Mark OJ 
Published: September 2006

Abstract
The nucleolus is the nuclear subdomain that assembles ribosomal subunits in eukaryotic cells. Steps in assembly include transcription, modification and cleavage of preribosomal RNA and incorporation of ribosomal proteins and 5S ribosomal RNA into maturing preribosomal complexes.
Nucleolar Dominance
Authors: Pikaard Craig S 
Published: September 2006

Abstract
Nucleolar dominance is an epigenetic phenomenon in plant and animal hybrids that describes the failure to form nucleoli, the sites of ribosome synthesis, on chromosomes inherited from one parent. The molecular basis for nucleolar dominance is the reversible silencing of ribosomal RNA genes transcribed by RNA polymerase I. These genes are clustered at loci spanning millions of base pairs, making nucleolar dominance one of the most extensive known chromosomal‐silencing phenomena.
Skeletogenesis: Genetics
Authors: Hogendoorn Pancras CW , Bovée Judith VMG , Karperien Marcel , Cleton‐Jansen Anne‐Marie 
Published: September 2006

Abstract
Skeletogenesis is a tightly regulated process during fetal, postnatal and pubertal growth, finely orchestrated by transcription factors and consecutive signaling pathways and controlled by delicate feedback loops. There is an increasing awareness of the role of these processes during tumorigenesis of primary bone tumors.
Attention Deficit–Hyperactivity Disorder (ADHD)
Authors: Todd Richard D 
Published: September 2006

Abstract
Attention deficit–hyperactivity disorder (ADHD) comprises a common and highly heritable group of syndromes with childhood onset that are characterized by impairments in attention span, impulse control and/or activity level. Neurobehavioral, imaging, treatment and candidate gene studies are most consistent with the clinical symptoms of ADHD being caused by abnormalities of the ventral projections of catecholamine pathways in the brain.
Muscular Dystrophies
Authors: Bushby Kate 
Published: September 2006

Abstract
The identification of the many genes involved in producing a muscular dystrophy phenotype has highlighted the complex molecular pathology of this group of diseases. Genetic and phenotypic heterogeneity is the norm, with mutations now described in proteins involved in many areas of key function in skeletal muscle, including proteins of the muscle fiber membrane, extracellular matrix, nuclear envelope and sarcomere.
Histone Acetylation and Disease
Authors: Harel‐Bellan Annick , Guasconi Valentina , Fritsch Lauriane , Sekhri Redha , Lehrmann Heike , Ait‐Si‐Ali Slimane 
Published: September 2006

Abstract
Acetylation of nucleosomal core histones plays a key regulatory role in many physiological processes such as proliferation and differentiation. Aberrant acetylation or deacetylation of histones leads to severe human diseases such as leukemia, epithelial cancers, fragile X‐syndrome and Rubinstein–Taybi syndrome.
Pancreatic Cancer
Authors: Sakorafas George H 
Published: September 2006

Abstract

Knowledge of the molecular biology of pancreatic cancer has grown rapidly. Genetic alterations in pancreatic cancer include oncogene mutations (most commonly
KRAS2
mutations) and tumor suppressor gene alterations (mainly
TP53
,
CDKN2A
,
DCC
, etc.). The advances may have clinical implications in the management of patients with pancreatic cancer (diagnosis, therapy, prognosis).
Multidrug Resistance in Cancer: Genetics of ABC Transporters
Authors: Ishikawa Toshihisa 
Published: September 2006

Abstract
Multidrug resistance in human cancer is the major obstacle to long‐term, sustained response of a patient to chemotherapy. It has been convincingly documented that several adenosine triphosphate‐binding cassette transporters cause multidrug resistance in cancer cells by actively extruding the clinically administered chemotherapeutic drugs.
Myeloproliferative Diseases: Molecular Genetics
Authors: Albitar Maher 
Published: September 2006

Abstract
Chronic myeloproliferative disorders (MPDs) are characterized by clonal proliferation of differentiated myeloid cells. This uncontrolled proliferation manifests itself in an increase in maturing granulocytes, erythrocytes, platelets, eosinophils or basophils, or a combination of these cells.
Lesch–Nyhan Disease
Authors: Visser JE , Jinnah HA 
Published: September 2006

Abstract
Lesch–Nyhan disease is caused by an inherited deficiency of the purine salvage enzyme hypoxanthine guanine phosphoribosyltransferase. Affected individuals display hyperuricemia and specific neurobehavioral features, including a hyperkinetic movement disorder, behavioral disturbances and self‐injurious behavior, which are thought to be attributable to dysfunction of the basal ganglia dopamine system.
Nuclear Receptor Genes
Authors: Laudet Vincent 
Published: September 2006

AbstractNuclear receptors are ligand‐dependant transcription factors that can directly regulate target genes in response to hormonal ligands, such as steroids, retinoic acid or thyroid hormones. They form a superfamily of genes that have a complex organization with most often alternative promoters, alternative splicing and autoregulation mechanisms. These genes are dispersed in metazoan genomes and their number varies widely from one genome to another (from 21 inDrosophilato about 270 in nematodes).
DNA Methylation: Enzymology
Authors: Szyf Moshe 
Published: September 2006

Abstract

In vertebrates, the dinucleotide sequence CG is methylated. The DNA methylation reaction is catalyzed by DNA methyltransferases, which use
S
‐adenosyl‐methionine as the methyl donor. In addition to DNA methyltransferases, chromatin modifying and remodeling proteins are involved in creating and replicating DNA methylation patterns. Data suggest that demethylases, enzymes that remove methyl groups from DNA, are involved in shaping DNA methylation patterns.
Transcriptomics and Proteomics: Integration?
Authors: Honoré Bent , Østergaard Morten 
Published: September 2006

Abstract
The genes are transcribed to pre‐messenger RNA, further processed to messenger RNA (transcripts), and finally translated into protein. The transcriptome constitutes the complete set of different transcripts that is synthesized in the lifetime of a cell or a tissue. The proteome refers to the complete set of proteins that is expressed, and modified following expression in the lifetime of a cell or a given tissue. Transcriptomics refers to the study of the transcriptome, while proteomics refers to the study of the proteome using large‐scale technologies for transcript or protein analyses. The two disciplines each provide unique information and supplement each other.
Proteomics: A Shotgun Approach without Two‐dimensional Gels
Authors: Delahunty Claire , Yates John R 
Published: September 2006

Abstract
Proteome analysis has been most commonly accomplished by the combination of two‐dimensional electrophoresis and mass spectrometry, but this method suffers some drawbacks that limit its usefulness for large‐scale analysis. New ‘shotgun’ techniques allow for the detection of proteins from complex mixtures and are rapidly replacing gel‐based methods for certain applications.
Promotion of axonal maturation and prevention of memory loss in mice by extracts of Astragalus mongholicus
Authors: Tohda C , Tamura T , Matsuyama S , Komatsu K 
Published: September 2006

Background and purpose:Neurons with atrophic neurites may remain alive and therefore may have the potential to regenerate even when neuronal death has occurred in some parts of the brain. This study aimed to explore effects of drugs that can facilitate the regeneration of neurites and the reconstruction of synapses even in severely damaged neurons.Experimental approach:We investigated the effects of extracts of Astragalus mongholicus on the cognitive defect in mice caused by injection with the amyloid peptide Aβ(25‐35). We also examined the effect of the extract on the regeneration of neurites and the reconstruction of synapses in cultured neurons damaged by Aβ(25‐35).Key results:A. mongholicus extract (1 g kg−1 day−1 for 15 days, p.o.) reversed Aβ(25‐35)‐induced memory loss and prevented the loss of axons and synapses in the cerebral cortex and hippocampus in mice. Treatment with Aβ(25‐35) (10 μM) induced axonal atrophy and synaptic loss in cultured rat cortical neurons. Subsequent treatment with A. mongholicus extract (100 μg/ml) resulted in significant axonal regeneration, reconstruction of neuronal synapses, and prevention of Aβ(25‐35)‐induced neuronal death. Similar extracts of A. membranaceus had no effect on axonal atrophy, synaptic loss, or neuronal death. The major known components of the extracts (astragalosides I, II, and IV) reduced neurodegeneration, but the activity of the extracts did not correlate with their content of these three astragalosides.Conclusion and implications:A. mongholicus is an important candidate for the treatment of memory disorders and the main active constituents may not be the known astragalosides.British Journal of Pharmacology (2006) 149, 532–541. doi:10.1038/sj.bjp.0706865
Hierarchical and multi-resolution representation of protein flexibility
Authors: Zhao Yong , Stoffler Daniel , Sanner Michel 
Published: September 2006

Abstract
Motivation: Conformational rearrangements during molecular interactions are observed in a wide range of biological systems. However, computational methods that aim at simulating and predicting molecular interactions are still largely ignoring the flexible nature of biological macromolecules as the number of degrees of freedom is computationally intractable when using brute force representations.
Results: In this article, we present a computational data structure called the Flexibility Tree (FT) that enables a multi-resolution and hierarchical encoding of molecular flexibility. This tree-like data structure allows the encoding of relatively small, yet complex sub-spaces of a protein's conformational space. These conformational sub-spaces are parameterized by a small number of variables and can be searched efficiently using standard global search techniques. The FT structure makes it straightforward to combine and nest a wide variety of motion types such as hinge, shear, twist, screw, rotameric side chains, normal modes and essential dynamics. Moreover, the ability to assign shapes to the nodes in a FT allows the interactive manipulation of flexible protein shapes and the interactive visualization of the impact of conformational changes on the protein's overall shape. We describe the design of the FT and illustrate the construction of such trees to hierarchically combine motion information obtained from a variety of sources ranging from experiment to user intuition, and describing conformational changes at different biological scales. We show that the combination of various types of motion helps refine the encoded conformational sub-spaces to include experimentally determined structures, and we demonstrate searching these sub-spaces for specific conformations.
Contact: sanner@scripps.edu
Supplementary information: Supplementary Data are available at Bioinformatics online.
Localization of Green Fluorescent Protein Fusions with the Seven Arabidopsis Vacuolar Sorting Receptors to Prevacuolar Compartments in Tobacco BY-2 Cells
Authors: Miao Yansong , Yan Pak Kan , Kim Hyeran , Hwang Inhwan , Jiang Liwen 
Published: September 2006

Abstract
We have previously demonstrated that vacuolar sorting receptor (VSR) proteins are concentrated on prevacuolar compartments (PVCs) in plant cells. PVCs in tobacco (Nicotiana tabacum) BY-2 cells are multivesicular bodies (MVBs) as defined by VSR proteins and the BP-80 reporter, where the transmembrane domain (TMD) and cytoplasmic tail (CT) sequences of BP-80 are sufficient and specific for correct targeting of the reporter to PVCs. The genome of Arabidopsis (Arabidopsis thaliana) contains seven VSR proteins, but little is known about their individual subcellular localization and function. Here, we study the subcellular localization of the seven Arabidopsis VSR proteins (AtVSR1–7) based on the previously proven hypothesis that the TMD and CT sequences correctly target individual VSR to its final destination in transgenic tobacco BY-2 cells. Toward this goal, we have generated seven chimeric constructs containing signal peptide (sp) linked to green fluorescent protein (GFP) and TMD/CT sequences (sp-GFP-TMD/CT) of the seven individual AtVSR. Transgenic tobacco BY-2 cell lines expressing these seven sp-GFP-TMD-CT fusions all exhibited typical punctate signals colocalizing with VSR proteins by confocal immunofluorescence. In addition, wortmannin caused the GFP-marked prevacuolar organelles to form small vacuoles, and VSR antibodies labeled these enlarged MVBs in transgenic BY-2 cells. Wortmannin also caused VSR-marked PVCs to vacuolate in other cell types, including Arabidopsis, rice (Oryza sativa), pea (Pisum sativum), and mung bean (Vigna radiata). Therefore, the seven AtVSRs are localized to MVBs in tobacco BY-2 cells, and wortmannin-induced vacuolation of PVCs is a general response in plants.
Divergence of the Dof Gene Families in Poplar, Arabidopsis, and Rice Suggests Multiple Modes of Gene Evolution after Duplication
Authors: Yang Xiaohan , Tuskan Gerald A. , Cheng (Max) Zong-Ming 
Published: September 2006

Abstract
It is widely accepted that gene duplication is a primary source of genetic novelty. However, the evolutionary fate of duplicated genes remains largely unresolved. The classical Ohno's Duplication-Retention-Non/Neofunctionalization theory, and the recently proposed alternatives such as subfunctionalization or duplication-degeneration-complementation, and subneofunctionalization, each can explain one or more aspects of gene fate after duplication. Duplicated genes are also affected by epigenetic changes. We constructed a phylogenetic tree using Dof (DNA binding with one finger) protein sequences from poplar (Populus trichocarpa) Torr. & Gray ex Brayshaw, Arabidopsis (Arabidopsis thaliana), and rice (Oryza sativa). From the phylogenetic tree, we identified 27 pairs of paralogous Dof genes in the terminal nodes. Analysis of protein motif structure of the Dof paralogs and their ancestors revealed six different gene fates after gene duplication. Differential protein methylation was revealed between a pair of duplicated poplar Dof genes, which have identical motif structure and similar expression pattern, indicating that epigenetics is involved in evolution. Analysis of reverse transcription-PCR, massively parallel signature sequencing, and microarray data revealed that the paralogs differ in expression pattern. Furthermore, analysis of nonsynonymous and synonymous substitution rates indicated that divergence of the duplicated genes was driven by positive selection. About one-half of the motifs in Dof proteins were shared by non-Dof proteins in the three plants species, indicating that motif co-option may be one of the forces driving gene diversification. We provided evidence that the Ohno's Duplication-Retention-Non/Neofunctionalization, subfunctionalization/duplication-degeneration-complementation, and subneofunctionalization hypotheses are complementary with, not alternative to, each other.
Separation of Arabidopsis Pollen Tetrads Is Regulated by QUARTET1, a Pectin Methylesterase Gene
Authors: Francis Kirk E. , Lam Sandy Y. , Copenhaver Gregory P. 
Published: September 2006

Abstract
Arabidopsis (Arabidopsis thaliana) QUARTET (QRT) genes are required for pollen separation during normal floral development. In qrt mutants, the four products of microsporogenesis remain fused and pollen grains are released as tetrads. In Arabidopsis, tetrad analysis in qrt mutants has been used to map all five centromeres, easily distinguish sporophytic from gametophytic mutations, and accurately assess crossover interference. Using a combination of forward and reverse genetics, we have identified the gene responsible for the qrt1 phenotype. Annotation predicts that QRT1 encodes a pectin methylesterase (PME), and enzymatic assays of QRT1 expressed in Escherichia coli indicate that QRT1 has PME activity. Promoter and transcription analysis demonstrate QRT1 is expressed in anther tissues shortly after meiosis is complete. Unexpectedly, the QRT1 promoter is also active in a variety of developmentally unrelated tissues, including developing guard cells, the hypocotyl-root transition zone, areas of lateral root emergence, and floral nectaries. PMEs constitute a large gene family in Arabidopsis, are involved in cell wall loosening, and have been implicated in various aspects of floral development and pollen tube elongation. The identification of QRT1 as a PME contributes to our understanding of pollen development and may help to provide valuable genetic tools in other plant species.
Up-Regulation of 1-Deoxy-d-Xylulose-5-Phosphate Synthase Enhances Production of Essential Oils in Transgenic Spike Lavender
Authors: Muñoz-Bertomeu Jesús , Arrillaga Isabel , Ros Roc , Segura Juan 
Published: September 2006

AbstractSpike lavender (Lavandula latifolia) is an aromatic shrub cultivated worldwide for the production of essential oils. The major constituents of these oils are monoterpenes, which are obtained from isopentenyl diphosphate and dimethylallyl diphosphate precursors through the plastidial methylerythritol phosphate (MEP) pathway and/or the cytosolic mevalonate pathway. 1-Deoxy-d-xylulose-5-P synthase (DXS) catalyzes the first step of the MEP pathway. A cDNA coding for the Arabidopsis (Arabidopsis thaliana) DXS was constitutively expressed in spike lavender. Gas chromatography/mass spectrometry analyses revealed that transgenic plants accumulated significantly more essential oils compared to controls (from 101.5% to 359.0% and from 12.2% to 74.1% yield increase compared to controls in leaves and flowers, respectively). T0 transgenic plants were grown for 2 years, self-pollinated, and the T1 seeds obtained. The inheritance of the DXS transgene was studied in the T1 generation. The increased essential oil phenotype observed in the transgenic T0 plants was maintained in the progeny that inherited the DXS transgene. Total chlorophyll and carotenoid content in DXS progenies that inherited the transgene depended on the analyzed plant, showing either no variation or a significant decrease in respect to their counterparts without the transgene. Transgenic plants had a visual phenotype similar to untransformed plants (controls) in terms of morphology, growth habit, flowering, and seed germination. Our results demonstrate that the MEP pathway contributes to essential oil production in spike lavender. They also demonstrate that the DXS enzyme plays a crucial role in monoterpene precursor biosynthesis and, thus, in essential oil production in spike lavender. In addition, our results provide a strategy to increase the essential oil production in spike lavender by metabolic engineering of the MEP pathway without apparent detrimental effects on plant development and fitness.
CER4Encodes an Alcohol-Forming Fatty Acyl-Coenzyme A Reductase Involved in Cuticular Wax Production in Arabidopsis
Authors: Rowland Owen , Zheng Huanquan , Hepworth Shelley R. , Lam Patricia , Jetter Reinhard , Kunst Ljerka 
Published: September 2006

AbstractA waxy cuticle that serves as a protective barrier against uncontrolled water loss and environmental damage coats the aerial surfaces of land plants. It is composed of a cutin polymer matrix and waxes. Cuticular waxes are complex mixtures of very-long-chain fatty acids and their derivatives. We report here the molecular cloning and characterization of CER4, a wax biosynthetic gene from Arabidopsis (Arabidopsis thaliana). Arabidopsis cer4 mutants exhibit major decreases in stem primary alcohols and wax esters, and slightly elevated levels of aldehydes, alkanes, secondary alcohols, and ketones. This phenotype suggested that CER4 encoded an alcohol-forming fatty acyl-coenzyme A reductase (FAR). We identified eight FAR-like genes in Arabidopsis that are highly related to an alcohol-forming FAR expressed in seeds of jojoba (Simmondsia chinensis). Molecular characterization of CER4 alleles and genomic complementation revealed that one of these eight genes, At4g33790, encoded the FAR required for cuticular wax production. Expression of CER4 cDNA in yeast (Saccharomyces cerevisiae) resulted in the accumulation of C24:0 and C26:0 primary alcohols. Fully functional green fluorescent protein-tagged CER4 protein was localized to the endoplasmic reticulum in yeast cells by confocal microscopy. Analysis of gene expression by reverse transcription-PCR indicated that CER4 was expressed in leaves, stems, flowers, siliques, and roots. Expression of a β-glucuronidase reporter gene driven by the CER4 promoter in transgenic plants was detected in epidermal cells of leaves and stems, consistent with a dedicated role for CER4 in cuticular wax biosynthesis. CER4 was also expressed in all cell types in the elongation zone of young roots. These data indicate that CER4 is an alcohol-forming FAR that has specificity for very-long-chain fatty acids and is responsible for the synthesis of primary alcohols in the epidermal cells of aerial tissues and in roots.
The Role of Cytosolic α-Glucan Phosphorylase in Maltose Metabolism and the Comparison of Amylomaltase in Arabidopsis and Escherichia coli
Authors: Lu Yan , Steichen Jon M. , Yao Jian , Sharkey Thomas D. 
Published: September 2006

Abstract
Transitory starch of leaves is broken down hydrolytically, making maltose the predominant form of carbon exported from chloroplasts at night. Maltose metabolism in the cytoplasm of Escherichia coli requires amylomaltase (MalQ) and maltodextrin phosphorylase (MalP). Possible orthologs of MalQ and MalP in the cytosol of Arabidopsis (Arabidopsis thaliana) were proposed as disproportionating enzyme (DPE2, At2g40840) and α-glucan phosphorylase (AtPHS2, At3g46970). In this article, we measured the activities of recombinant DPE2 and AtPHS2 proteins with various substrates; we show that maltose and a highly branched, soluble heteroglycan (SHG) are excellent substrates for DPE2 and propose that a SHG is the in vivo substrate for DPE2 and AtPHS2. In E. coli, MalQ and MalP preferentially use smaller maltodextrins (G3–G7) and we suggest that MalQ and DPE2 have similar, but nonidentical, roles in maltose metabolism. To study this, we complemented a MalQ− E. coli strain with DPE2 and found that the rescue was not complete. To investigate the role of AtPHS2 in maltose metabolism, we characterized a T-DNA insertion line of the AtPHS2 gene. The nighttime maltose level increased 4 times in the Atphs2-1 mutant. The comparison of maltose metabolism in Arabidopsis with that in E. coli and the comparison of the maltose level in plants lacking DPE2 or AtPHS2 indicate that an alternative route to metabolize the glucan residues in SHG exists. Other plant species also contain SHG, DPE2, and α-glucan phosphorylase, so this pathway for maltose metabolism may be widespread among plants.