bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aurivillius Phases in the Bi4Ti3O12/BiFeO3 System: Thermal Behaviour and Crystal Structure
Authors: Krzhizhanovskaya M. , Filatov S. , Gusarov V. , Paufler P. , Bubnova R. , Morozov M. , Meyer D. C. 
Published: May 2005

AbstractFour compounds of the Bi4Ti3O12/BiFeO3 system with the formula Bi2Bin−1(Ti,Fe)nO3n+3, n = 3, 4, 4.5 and 6 were studied using high‐temperature X‐ray powder diffraction and differential thermoanalysis methods. The crystal structure of the n = 6 phase was refined by the Rietveld method. An unusual behaviour of thermal expansion attributed to an orthorhombic‐to‐tetragonal transformation was revealed. For all the compounds, the lattice parameter c vs temperature T dependence has three regions in the range of T = 20 –750 °C interpreted as (1) expansion of the initial orthorhombic phase, (2) a pronounced structure reconstruction to the tetragonal phase, (3) an expansion of the tetragonal phase.The crystal structure of Bi7Ti3Fe3O21 based on 6‐layer‐perovskite blocks is proposed from X‐ray powder diffraction data. The Rietveld refinement of the structure in the orthorhombic space group F2mm with lattice parameters a = 5.4699(3), b = 5.4924(3), c = 57.551(3) Å (Rp = 9.4, Rwp = 11.9, Rexp = 4.7, RB = 4.4 %) shows that a distorted 6‐layer model fits the data of Bi7Ti3Fe3O21.
Pancreatic apudomas
Authors: Bloom S. R. , Polak J. M. , Welbourn R. B. 
Published: May 2005

AbstractPancreatic apudomas are not common but are frequently curable. Thus, it is important for every clinician to be fully aware of the varied clinical syndromes that suggest their presence. The availability of specific radioimmunoassays has made confirmation of the diagnosis relatively simple. Advances in the techniques for staining the different cell types have led to the recognition that many of these tumors are mixed, and that the general term “pancreatic apudoma” is appropriate. Pancreatic endocrine tumors, as examples of “nature's experiments,” have yielded considerable insight into the possible physiologic effects of the various peptides they produce. It is to be hoped that further study of tumors such as the somatostatinoma and PPoma may yield further information about these enigmatic compounds.
THE RAGE OF PARLIAMENTS: THE HOUSE OF COMMONS, 1690–1715
Authors: JACKSON CLARE 
Published: May 2005

The history of parliament: the House of Commons, 1690–1715. Edited by Eveline Cruickshanks, Stuart Handley, and D. W. Hayton. Cambridge: Cambridge University Press, 2002. 5 vols. i: Introductory survey (pp. xvi+958 and CD-ROM); ii: Constituencies (pp. xvi+945); iii: Members A–F (pp. xvi+1,134); iv: Members G–N (pp. xvi+1,052); v: Members O–Z (pp. xvi+962). ISBN 0-521-77221-4. £250.00 (introductory price); thereafter £300.00.The publication of these five volumes represents the eighth contribution to the History of Parliament Trust's record of the House of Commons that now extends to twenty-eight volumes containing nearly twenty million words in over 20,000 pages. According to the Trust's chairman, Ted Rowlands MP, completing these volumes that cover the period 1690–1715 ‘has been a thirty-year odyssey’ (i, p. xi) successively directed by Eveline Cruickshanks and David Hayton as editors and Stuart Handley as associate editor. Their appearance completes the Trust's history of the Commons during the ‘long eighteenth century’ from Charles II's restoration in 1660 to George IV's death in 1820, whilst the periods 1384–1421 and 1509–1603 are covered in previously published volumes. In 1998, all the information contained in the twenty-three extant volumes was incorporated into a single text-file CD-ROM with various electronic search functions. Compiled by a team of fourteen distinguished contributors, the format of the volumes here reviewed follows that of earlier publications by the Trust. The first comprises a masterful ‘introductory survey’ by Hayton that extends to over 500 pages with twenty-seven appendices and confers coherence on the other volumes by enumerating the diverse range of constituency customs, election procedures, membership, organization, and activities characteristic of the Commons between 1690 and 1715. The second contains detailed profiles of the 317 English, Welsh, and Scottish constituencies, whilst the remaining three supply biographical entries of the 1,982 Members who sat in the Commons during this period.
SECISDesign: a server to design SECIS-elements within the coding sequence
Authors: Busch Anke , Will Sebastian , Backofen Rolf 
Published: May 2005

Abstract
Summary: SECISDesign is a server for the design of SECIS-elements and arbitrary RNA-elements within the coding sequence of an mRNA. The element has to satisfy both structure and sequence constraints. At the same time, a certain amino acid similarity to the original protein has to be kept. The designed sequence can be used for recombinant expression of selenoproteins in Escherichia coli.
Availability: The server is available at http://www.bio.inf.uni-jena.de/Software/SECISDesign/index.html
Contact: backofen@inf.uni-jena.de
Functional annotation from predicted protein interaction networks
Authors: McDermott Jason , Bumgarner Roger , Samudrala Ram 
Published: May 2005

AbstractMotivation: Progress in large-scale experimental determination of protein–protein interaction networks for several organisms has resulted in innovative methods of functional inference based on network connectivity. However, the amount of effort and resources required for the elucidation of experimental protein interaction networks is prohibitive. Previously we, and others, have developed techniques to predict protein interactions for novel genomes using computational methods and data generated from other genomes.Results: We evaluated the performance of a network-based functional annotation method that makes use of our predicted protein interaction networks. We show that this approach performs equally well on experimentally derived and predicted interaction networks, for both manually and computationally assigned annotations. We applied the method to predicted protein interaction networks for over 50 organisms from all domains of life, providing annotations for many previously unannotated proteins and verifying existing low-confidence annotations.Availability: Functional predictions for over 50 organisms are available at http://bioverse.compbio.washington.edu and datasets used for analysis at http://data.compbio.washington.edu/misc/downloads/nannotation_data/Contact: admin@bioverse.compbio.washington.eduSupplementary information: A supplemental appendix gives additional details not in the main text. (http://data.compbio.washington.edu/misc/downloads/nannotation_data/supplement.pdf).
A latent variable model for chemogenomic profiling
Authors: Flaherty Patrick , Giaever Guri , Kumm Jochen , Jordan Michael I. , Arkin Adam P. 
Published: May 2005

AbstractMotivation: In haploinsufficiency profiling data, pleiotropic genes are often misclassified by clustering algorithms that impose the constraint that a gene or experiment belong to only one cluster. We have developed a general probabilistic model that clusters genes and experiments without requiring that a given gene or drug only appear in one cluster. The model also incorporates the functional annotation of known genes to guide the clustering procedure.Results: We applied our model to the clustering of 79 chemogenomic experiments in yeast. Known pleiotropic genes PDR5 and MAL11 are more accurately represented by the model than by a clustering procedure that requires genes to belong to a single cluster. Drugs such as miconazole and fenpropimorph that have different targets but similar off-target genes are clustered more accurately by the model-based framework. We show that this model is useful for summarizing the relationship among treatments and genes affected by those treatments in a compendium of microarray profiles.Availability: Supplementary information and computer code at http://genomics.lbl.gov/lldaContact: flaherty@berkeley.edu
Prevalence of quadruplexes in the human genome
Authors: Huppert Julian L. , Balasubramanian Shankar 
Published: May 2005

Abstract
Guanine-rich DNA sequences of a particular form have the ability to fold into four-stranded structures called G-quadruplexes. In this paper, we present a working rule to predict which primary sequences can form this structure, and describe a search algorithm to identify such sequences in genomic DNA. We count the number of quadruplexes found in the human genome and compare that with the figure predicted by modelling DNA as a Bernoulli stream or as a Markov chain, using windows of various sizes. We demonstrate that the distribution of loop lengths is significantly different from what would be expected in a random case, providing an indication of the number of potentially relevant quadruplex-forming sequences. In particular, we show that there is a significant repression of quadruplexes in the coding strand of exonic regions, which suggests that quadruplex-forming patterns are disfavoured in sequences that will form RNA.
Two Microtubule-Associated Proteins of the Arabidopsis MAP65 Family Function Differently on Microtubules
Authors: Mao Tonglin , Jin Lifeng , Li Hua , Liu Bo , Yuan Ming 
Published: May 2005

Abstract
The organization and dynamics of microtubules are regulated by microtubule-associated proteins, or MAPs. In Arabidopsis (Arabidopsis thaliana), nine genes encode proteins of the evolutionarily conserved MAP65 family. We proposed that different MAP65s might have distinct roles in the interaction with microtubules. In this study, two AtMAP65 proteins, AtMAP65-1 and AtMAP65-6, were chosen to test this hypothesis in vitro. Although both fusion proteins were able to cosediment with microtubules in vitro, different properties on tubulin polymerization and microtubule bundling were observed. AtMAP65-1 was able to promote tubulin polymerization, enhance microtubule nucleation, and decrease the critical concentration for tubulin polymerization. It also induced the formation of large microtubule bundles by forming cross-bridges between microtubules evenly along the whole length of microtubules. In the presence of AtMAP65-1, microtubule bundles were more resistant to cold and dilution treatments. AtMAP65-6, however, demonstrated no activity in promoting tubulin polymerization and stabilizing preformed microtubules. AtMAP65-6 induced microtubules to form a mesh-like network with individual microtubules. Cross-bridge-like interactions were only found at regional sites between microtubules. The microtubule network induced by AtMAP65-6 was more resistant to high concentration of NaCl than the bundles induced by AtMAP65-1. Purified monospecific anti-AtMAP65-6 antibodies revealed that AtMAP65-6 was associated with mitochondria in Arabidopsis cells. It was concluded that these two MAP65 proteins were targeted to distinct sites, thus performing distinct functions in Arabidopsis cells.
Tripeptidyl Peptidase II. An Oligomeric Protease Complex from Arabidopsis
Authors: Book Adam J. , Yang Peizhen , Scalf Mark , Smith Lloyd M. , Vierstra Richard D. 
Published: May 2005

Abstract
The breakdown of most nuclear and cytoplasmic proteins involves their partial cleavage by the 26S proteasome followed by further disassembly to free amino acids by the combined action of endo- and exopeptidases. In animals, one important intermediate exopeptidase is tripeptidyl peptidase (TPP)II, which digests peptide products of the 26S proteasome and other endopeptidases into tripeptides. Here, we describe the purification and characterization of TPPII from Arabidopsis (Arabidopsis thaliana). Like its animal counterparts, Arabidopsis TPPII exists as a soluble, approximately 5- to 9-MD complex. Two related species of 153 and 142 kD are present in the purified preparations that are derived from a single TPP2 gene. Sequencing by Edman degradation of the intact polypeptides and mass spectrometry of proteolytic fragments demonstrated that the 142-kD form mainly differs from the 153-kD form by a truncation at the C-terminal end. This serine protease is a member of the subtilisin superfamily and is sensitive to the inhibitors alanine-alanine-phenylalanine-chloromethylketone and butabindide, which are diagnostic for the TPPII subfamily. The Arabidopsis TPP2 gene is widely expressed in many tissue types with related genes evident in other plant genomes. Whereas the 26S proteasome is essential, TPPII appears not as important for plant physiology. An Arabidopsis T-DNA mutant defective in TPP2 expression displays no phenotypic abnormalities and is not hypersensitive to either amino acid analogs or the 26S proteasome inhibitor MG132. As a consequence, plants likely contain other intermediate exopeptidases that assist in amino acid recycling.
Gene Family Analysis of the Arabidopsis Pollen Transcriptome Reveals Biological Implications for Cell Growth, Division Control, and Gene Expression Regulation
Authors: Pina Cristina , Pinto Francisco , Feijó José A. , Becker Jörg D. 
Published: May 2005

AbstractUpon germination, pollen forms a tube that elongates dramatically through female tissues to reach and fertilize ovules. While essential for the life cycle of higher plants, the genetic basis underlying most of the process is not well understood. We previously used a combination of flow cytometry sorting of viable hydrated pollen grains and GeneChip array analysis of one-third of the Arabidopsis (Arabidopsis thaliana) genome to define a first overview of the pollen transcriptome. We now extend that study to approximately 80% of the genome of Arabidopsis by using Affymetrix Arabidopsis ATH1 arrays and perform comparative analysis of gene family and gene ontology representation in the transcriptome of pollen and vegetative tissues. Pollen grains have a smaller and overall unique transcriptome (6,587 genes expressed) with greater proportions of selectively expressed (11%) and enriched (26%) genes than any vegetative tissue. Relative gene ontology category representations in pollen and vegetative tissues reveal a functional skew of the pollen transcriptome toward signaling, vesicle transport, and the cytoskeleton, suggestive of a commitment to germination and tube growth. Cell cycle analysis reveals an accumulation of G2/M-associated factors that may play a role in the first mitotic division of the zygote. Despite the relative underrepresentation of transcription-associated transcripts, nonclassical MADS box genes emerge as a class with putative unique roles in pollen. The singularity of gene expression control in mature pollen grains is further highlighted by the apparent absence of small RNA pathway components.
An Expression and Bioinformatics Analysis of the Arabidopsis Serine Carboxypeptidase-Like Gene Family
Authors: Fraser Christopher M. , Rider Lance W. , Chapple Clint 
Published: May 2005

Abstract
The Arabidopsis (Arabidopsis thaliana) genome encodes a family of 51 proteins that are homologous to known serine carboxypeptidases. Based on their sequences, these serine carboxypeptidase-like (SCPL) proteins can be divided into several major clades. The first group consists of 21 proteins which, despite the function implied by their annotation, includes two that have been shown to function as acyltransferases in plant secondary metabolism: sinapoylglucose:malate sinapoyltransferase and sinapoylglucose:choline sinapoyltransferase. A second group comprises 25 SCPL proteins whose biochemical functions have not been clearly defined. Genes encoding representatives from both of these clades can be found in many plants, but have not yet been identified in other phyla. In contrast, the remaining SCPL proteins include five members that are similar to serine carboxypeptidases from a variety of organisms, including fungi and animals. Reverse transcription PCR results suggest that some SCPL genes are expressed in a highly tissue-specific fashion, whereas others are transcribed in a wide range of tissue types. Taken together, these data suggest that the Arabidopsis SCPL gene family encodes a diverse group of enzymes whose functions are likely to extend beyond protein degradation and processing to include activities such as the production of secondary metabolites.
Identification of cis-Elements That Regulate Gene Expression during Initiation of Axillary Bud Outgrowth in Arabidopsis
Authors: Tatematsu Kiyoshi , Ward Sally , Leyser Ottoline , Kamiya Yuji , Nambara Eiji 
Published: May 2005

Abstract
Growth regulation associated with dormancy is an essential element in plant life cycles. To reveal regulatory mechanisms of bud outgrowth, we analyzed transcriptomes of axillary shoots before and after main stem decapitation in Arabidopsis (Arabidopsis thaliana). We searched for any enriched motifs among the upstream regions of up-regulated and down-regulated genes after decapitation. The promoters of down-regulated genes were enriched for TTATCC motifs that resemble the sugar-repressive element, whereas the promoters of up-regulated genes were enriched for GGCCCAWW and AAACCCTA, designated Up1 and Up2, respectively. Transgenic plants harboring a reporter gene driven by a tandem repeat of the elements were produced to analyze their function in vivo. Sugar-repressive element-mediated gene expression was down-regulated by the application of sugars but was unaffected after decapitation. In contrast, expression driven by the repeat containing both Up1 and Up2 was up-regulated after decapitation, although the Up1 or Up2 repeat alone failed to induce reporter gene expression in axillary shoots. In addition, disruption of both Up1 and Up2 elements in a ribosomal protein gene abolished the decapitation-induced expression. Ontological analysis demonstrated that up-regulated genes with Up elements were disproportionately predicted to function in protein synthesis and cell cycle. Up1 is similar to an element known to be a potential target for TCP (TEOSINTE BRANCHED1, CYCLOIDEA, PCFs family) transcription factor(s), which regulate expression of cell cycle-related and ribosomal protein genes. Our data indicate that Up1-mediated transcription of protein synthesis and cell cycle genes is an important regulatory step during the initiation of axillary shoot outgrowth induced by decapitation.
Brassinosteroid Homeostasis in Arabidopsis Is Ensured by Feedback Expressions of Multiple Genes Involved in Its Metabolism
Authors: Tanaka Kiwamu , Asami Tadao , Yoshida Shigeo , Nakamura Yasushi , Matsuo Tomoaki , Okamoto Shigehisa 
Published: May 2005

AbstractHomeostasis of brassinosteroids (BRs) is essential for normal growth and development in higher plants. We examined responsiveness of 11 BR metabolic gene expressions to the decrease or increase of endogenous BR contents in Arabidopsis (Arabidopsis thaliana) to expand our knowledge of molecular mechanisms underlying BR homeostasis. Five BR-specific biosynthesis genes (DET2, DWF4, CPD, BR6ox1, and ROT3) and two sterol biosynthesis genes (FK and DWF5) were up-regulated in BR-depleted wild-type plants grown under brassinazole, a BR biosynthesis inhibitor. On the other hand, in BR-excessive wild-type plants that were fed with brassinolide, four BR-specific synthesis genes (DWF4, CPD, BR6ox1, and ROT3) and a sterol synthesis gene (DWF7) were down-regulated and a BR inactivation gene (BAS1) was up-regulated. However, their response to fluctuation of BR levels was highly reduced (DWF4) or nullified (the other eight genes) in a bri1 mutant. Taken together, our results imply that BR homeostasis is maintained through feedback expressions of multiple genes, each of which is involved not only in BR-specific biosynthesis and inactivation, but also in sterol biosynthesis. Our results also indicate that their feedback expressions are under the control of a BRI1-mediated signaling pathway. Moreover, a weak response in the mutant suggests that DWF4 alone is likely to be regulated in other way(s) in addition to BRI1 mediation.
New Arabidopsis Recombinant Inbred Lines (Landsberg erecta × Nossen) Reveal Natural Variation in Phytochrome-Mediated Responses
Authors: Magliano Teresa M. Alconada , Botto Javier F. , Godoy A. Veronica , Symonds V. Vaughan , Lloyd Alan M. , Casal Jorge J. 
Published: May 2005

Abstract
We used 52 Arabidopsis (Arabidopsis thaliana) accessions and developed a new set of 137 recombinant inbred lines between Landsberg erecta (Ler) and Nossen (No-0) to explore the genetic basis of phytochrome-mediated responses during deetiolation. Unexpectedly, most accessions showed weak or moderate hypocotyl growth and cotyledon unfolding responses to pulses of far-red light (FR). Crosses between Columbia and No-0, two accessions with poor response, segregated seedlings with unfolded cotyledons under pulsed FR, suggesting the occurrence of accession-specific loci in the repression of morphological responses to weak light signals. Confirming the latter expectation, mapping of responses to pulsed FR in the Ler × No-0 lines identified novel loci. Despite its weak response to pulsed FR, No-0 showed a response to continuous FR stronger than that observed in Ler. By mapping the differential effect of pulsed versus continuous FR, we identified two high-irradiance response loci that account for the steeper response to continuous FR in No-0. This underscores the potential of the methodology to identify loci involved in the regulation of the shape of signal input-output relationships. Loci specific for a given phytochrome-mediated response were more frequent than pleiotropic loci. Segregation of these specific loci is predicted to yield different combinations of seedling responsivity to light. Such flexibility in combination of responses is observed among accessions and could aid in the adjustment to different microenvironments.
Roles of Arabidopsis AtREV1 and AtREV7 in Translesion Synthesis
Authors: Takahashi Shinya , Sakamoto Ayako , Sato Shusei , Kato Tomohiko , Tabata Satoshi , Tanaka Atsushi 
Published: May 2005

Abstract
Plants have mechanisms for repairing and tolerating detrimental effects by various DNA damaging agents. A tolerance pathway that has been predicted to be present in higher plants is translesion synthesis (TLS), which is catalyzed by polymerases. In Arabidopsis (Arabidopsis thaliana), however, the only gene known to be involved in TLS is the Arabidopsis homolog of REV3, AtREV3, which is a putative catalytic subunit of Arabidopsis DNA polymerase ζ. A disrupted mutant of AtREV3, rev3, was previously found to be highly sensitive to ultraviolet-B (UV-B) and various DNA damaging agents. REV1 and REV7 are thought to be components of translesion synthesis in plants. In this study, we identified the Arabidopsis homologs of REV1 and REV7 (AtREV1 and AtREV7). Several mutants carrying disrupted AtREV1 and AtREV7 genes were isolated from Arabidopsis T-DNA-inserted lines. An AtREV1-disrupted mutant, rev1, was found to be moderately sensitive to UV-B and DNA cross-linkers. A rev1rev3 double mutant, like rev3, showed high sensitivity to UV-B, γ-rays, and DNA cross-linkers. An AtREV7-disrupted mutant, rev7, was possibly sensitive to cis-diamminedichloroplatinum(II), a kind of DNA cross-linker, but it was not sensitive to acute UV-B and γ-ray irradiation. On the other hand, the aerial growth of rev7, like the aerial growth of rev1 and rev3, was inhibited by long-term UV-B. These results suggest that a TLS mechanism exists in a higher plant and show that AtREV1 and AtREV7 have important roles in tolerating exposure to DNA-damaging agents.