bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pattern of Organization of Human Mitochondrial Pseudogenes in the Nuclear Genome
Authors: Woischnik Markus , Moraes Carlos T. 
Published: July 2008

Mitochondrial pseudogenes in the human nuclear genome have been previously described, mostly as a source of artifacts during the analysis of the mitochondrial genome. With the availability of the complete human genome sequence, we performed a comprehensive analysis of mtDNA insertions into the nucleus. We found 612 independent integrations that are evenly distributed among all chromosomes as well as within each individual chromosome. The identified pseudogenes account for a content of at least 0.016% of the human nuclear DNA. Up to 30% of a chromosome's mtDNA pseudogene content is composed of fragments that encompass two or more adjacent mitochondrial genes, and we found no correlation between the abundance of mitochondrial transcripts and the multiplicity of integrations. These observations indicate that the migrations of mitochondrial DNA sequences to the nucleus were predominantly DNA mediated. Phylogenetic analysis of the mtDNA pseudogenes and mtDNA sequences of primates indicate a continuous transfer into the nucleus. Because of the limited window of opportunity for mtDNA transfer to the germline, sperm mtDNA, which is released from degenerating mitochondria after fertilization, could be an important source of nuclear mtDNA pseudogenes.[Online supplemental material available athttp://www.genome.org]
Multiplex Three-Dimensional Brain Gene Expression Mapping in a Mouse Model of Parkinson's Disease
Authors: Brown Vanessa M. , Ossadtchi Alex , Khan Arshad H. , Yee Simon , Lacan Goran , Melega William P. , Cherry Simon R. , Leahy Richard M. , Smith Desmond J. 
Published: July 2008

To facilitate high-throughput 3D imaging of brain gene expression, a new method called voxelation has been developed. Spatially registered voxels (cubes) are analyzed, resulting in multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging systems. Using microarrays, 40 voxel images for 9000 genes were acquired from brains of both normal mice and mice in which a pharmacological model of Parkinson's disease (PD) had been induced by methamphetamine. Quality-control analyses established the reproducibility of the voxelation procedure. The investigation revealed a common network of coregulated genes shared between the normal and PD brain, and allowed identification of putative control regions responsible for these networks. In addition, genes involved in cell/cell interactions were found to be prominently regulated in the PD brains. Finally, singular value decomposition (SVD), a mathematical method used to provide parsimonious explanations of complex data sets, identified gene vectors and their corresponding images that distinguished between normal and PD brain structures, most pertinently the striatum.[All study results and supplementary data are available on the web athttp://www.pharmacology.ucla.edu/smithlab/genome_multiplex and athttp://www.genome.org. Microarray data are also available at GEO,http://www.ncbi.nlm.nih.gov/geo, under the series accession no. GSE30.]
Long-Range Heterogeneity at the 3′ Ends of Human mRNAs
Authors: Iseli Christian , Stevenson Brian J. , de Souza Sandro J. , Samaia Helena B. , Camargo Anamaria A. , Buetow Kenneth H. , Strausberg Robert L. , Simpson Andrew J.G. , Bucher Philipp , Jongeneel C. Victor 
Published: July 2008

The publication of a draft of the human genome and of large collections of transcribed sequences has made it possible to study the complex relationship between the transcriptome and the genome. In the work presented here, we have focused on mapping mRNA 3′ ends onto the genome by use of the raw data generated by the expressed sequence tag (EST) sequencing projects. We find that at least half of the human genes encode multiple transcripts whose polyadenylation is driven by multiple signals. The corresponding transcript 3′ ends are spread over distances in the kilobase range. This finding has profound implications for our understanding of gene expression regulation and of the diversity of human transcripts, for the design of cDNA microarray probes, and for the interpretation of gene expression profiling experiments.[The following individuals kindly provided reagents, samples or unpublished information as indicated in the paper: G. Riggins, C. Ruegg, J.-B. Demoulin, P. Olsson, F. Funari, P. Schneider, L.F. Reis, and J.-C. Renauld]
A Computer-Based Method of Selecting Clones for a Full-Length cDNA Project: Simultaneous Collection of Negligibly Redundant and Variant cDNAs
Authors: Osato Naoki , Itoh Masayoshi , Konno Hideaki , Kondo Shinji , Shibata Kazuhiro , Carninci Piero , Shiraki Toshiyuki , Shinagawa Akira , Arakawa Takahiro , Kikuchi Shoshi , Sato Kouji , Kawai Jun , Hayashizaki Yoshihide 
Published: July 2008

We describe a computer-based method that selects representative clones for full-length sequencing in a full-length cDNA project. Our method classifies end sequences using two kinds of criteria, grouping, and clustering. Grouping places together variant cDNAs, family genes, and cDNAs with sequencing errors. Clustering separates those cDNA clones into distinct clusters. The full-length sequences of the clones selected by grouping are determined preferentially, and then the sequences selected by clustering are determined. Grouping reduced the number of rice cDNA clones for full-length sequencing to 21% and mouse cDNA clones to 25%. Rice full-length sequences selected by grouping showed a 1.07-fold redundancy. Mouse full-length sequences showed a 1.04-fold redundancy, which can be reduced by ∼30% from the selection using our previous method. To estimate the coverage of unique genes, we used FANTOM (Functional Annotation of RIKEN Mouse cDNA Clones) clusters (the RIKEN Genome Exploration Research Group 2001). Grouping covered almost all unique genes (93% of FANTOM clusters), and clustering covered all genes. Therefore, our method is useful for the selection of appropriate representative clones for full-length sequencing, thereby greatly reducing the cost, labor, and time necessary for this process.[The programs used in this paper are available online at http://genome.gsc.riken.go.jp/software/2C.]
Functional Analysis of Arabidopsis Postprenylation CaaX Processing Enzymes and Their Function in Subcellular Protein Targeting
Authors: Bracha-Drori Keren , Shichrur Keren , Lubetzky Tsofnat Cohen , Yalovsky Shaul 
Published: July 2008

Abstract
Prenylation is a posttranslational protein modification essential for developmental processes and response to abscisic acid. Following prenylation, the three C-terminal residues are proteoliticaly removed and in turn the free carboxyl group of the isoprenyl cysteine is methylated. The proteolysis and methylation, collectively referred to as CaaX processing, are catalyzed by Ste24 endoprotease or Rce1 endoprotease and by an isoprenyl cysteine methyltransferase (ICMT). Arabidopsis (Arabidopsis thaliana) contains single STE24 and RCE1 and two ICMT homologs. Here we show that in yeast (Saccharomyces cerevisiae) AtRCE1 promoted a-mating factor secretion and membrane localization of a ROP GTPase. Furthermore, green fluorescent protein fusion proteins of AtSTE24, AtRCE1, AtICMTA, and AtICMTB are colocalized in the endoplasmic reticulum, indicating that prenylated proteins reach this compartment and that CaaX processing is likely required for subcellular targeting. AtICMTB can process yeast a-factor more efficiently than AtICMTA. Sequence and mutational analyses revealed that the higher activity AtICMTB is conferred by five residues, which are conserved between yeast Ste14p, human ICMT, and AtICMTB but not in AtICMTA. Quantitative real-time reverse transcription-polymerase chain reaction and microarray data show that AtICMTA expression is significantly lower compared to AtICMTB. AtICMTA null mutants have a wild-type phenotype, indicating that its function is redundant. However, AtICMT RNAi lines had fasciated inflorescence stems, altered phylotaxis, and developed multiple buds without stem elongation. The phenotype of the ICMT RNAi lines is similar to farnesyltransferase β-subunit mutant enhanced response to abscisic acid2 but is more subtle. Collectively, the data suggest that AtICMTB is likely the major ICMT and that methylation modulates activity of prenylated proteins.
Monogalactosyldiacylglycerol Deficiency in Arabidopsis Affects Pigment Composition in the Prolamellar Body and Impairs Thylakoid Membrane Energization and Photoprotection in Leaves
Authors: Aronsson Henrik , Schöttler Mark A. , Kelly Amélie A. , Sundqvist Christer , Dörmann Peter , Karim Sazzad , Jarvis Paul 
Published: July 2008

AbstractMonogalactosyldiacylglycerol (MGDG) is the major lipid constituent of chloroplast membranes and has been proposed to act directly in several important plastidic processes, particularly during photosynthesis. In this study, the effect of MGDG deficiency, as observed in the monogalactosyldiacylglycerol synthase1-1 (mgd1-1) mutant, on chloroplast protein targeting, phototransformation of pigments, and photosynthetic light reactions was analyzed. The targeting of plastid proteins into or across the envelope, or into the thylakoid membrane, was not different from wild-type in the mgd1 mutant, suggesting that the residual amount of MGDG in mgd1 was sufficient to maintain functional targeting mechanisms. In dark-grown plants, the ratio of bound protochlorophyllide (Pchlide, F656) to free Pchlide (F631) was increased in mgd1 compared to the wild type. Increased levels of the photoconvertible pigment-protein complex (F656), which is photoprotective and suppresses photooxidative damage caused by an excess of free Pchlide, may be an adaptive response to the mgd1 mutation. Leaves of mgd1 suffered from a massively impaired capacity for thermal dissipation of excess light due to an inefficient operation of the xanthophyll cycle; the mutant contained less zeaxanthin and more violaxanthin than wild type after 60 min of high-light exposure and suffered from increased photosystem II photoinhibition. This is attributable to an increased conductivity of the thylakoid membrane at high light intensities, so that the proton motive force is reduced and the thylakoid lumen is less acidic than in wild type. Thus, the pH-dependent activation of the violaxanthin de-epoxidase and of the PsbS protein is impaired.
Induced Plant Defenses in the Natural Environment:Nicotiana attenuataWRKY3 and WRKY6 Coordinate Responses to Herbivory
Authors: Skibbe Melanie , Qu Nan , Galis Ivan , Baldwin Ian T. 
Published: July 2008

AbstractA plant-specific family of WRKY transcription factors regulates plant responses to pathogens and abiotic stresses. Here, we identify two insect-responsive WRKY genes in the native tobacco Nicotiana attenuata: WRKY3, whose transcripts accumulate in response to wounding, and WRKY6, whose wound responses are significantly amplified when fatty acid–amino acid conjugates (FACs) in larval oral secretions are introduced into wounds during feeding. WRKY3 is required for WRKY6 elicitation, yet neither is elicited by treatment with the phytohormone wound signal jasmonic acid. Silencing either WRKY3 or WRKY6, or both, by stable transformation makes plants highly vulnerable to herbivores under glasshouse conditions and in their native habitat in the Great Basin Desert, Utah, as shown in three field seasons. This susceptibility is associated with impaired jasmonate (JA) accumulation and impairment of the direct (trypsin proteinase inhibitors) and indirect (volatiles) defenses that JA signaling mediates. The response to wounding and herbivore-specific signals (FACs) demonstrates that these WRKYs help plants to differentiate mechanical wounding from herbivore attack, mediating a plant's herbivore-specific defenses. Differences in responses to single and multiple elicitations indicate an important role of WRKY3 and WRKY6 in potentiating and/or sustaining active JA levels during continuous insect attack.
SCREAM/ICE1andSCREAM2Specify Three Cell-State Transitional Steps Leading toArabidopsisStomatal Differentiation
Authors: Kanaoka Masahiro M. , Pillitteri Lynn Jo , Fujii Hiroaki , Yoshida Yuki , Bogenschutz Naomi L. , Takabayashi Junji , Zhu Jian-Kang , Torii Keiko U. 
Published: July 2008

AbstractDifferentiation of specialized cell types in multicellular organisms requires orchestrated actions of cell fate determinants. Stomata, valves on the plant epidermis, are formed through a series of differentiation events mediated by three closely related basic-helix-loop-helix proteins: SPEECHLESS (SPCH), MUTE, and FAMA. However, it is not known what mechanism coordinates their actions. Here, we identify two paralogous proteins, SCREAM (SCRM) and SCRM2, which directly interact with and specify the sequential actions of SPCH, MUTE, and FAMA. The gain-of-function mutation in SCRM exhibited constitutive stomatal differentiation in the epidermis. Conversely, successive loss of SCRM and SCRM2 recapitulated the phenotypes of fama, mute, and spch, indicating that SCRM and SCRM2 together determined successive initiation, proliferation, and terminal differentiation of stomatal cell lineages. Our findings identify the core regulatory units of stomatal differentiation and suggest a model strikingly similar to cell-type differentiation in animals. Surprisingly, map-based cloning revealed that SCRM is INDUCER OF CBF EXPRESSION1, a master regulator of freezing tolerance, thus implicating a potential link between the transcriptional regulation of environmental adaptation and development in plants.
Population structure of the parasitic nematodeAnguillicola crassus, an invader of declining North Atlantic eel stocks
Authors: WIELGOSS SÉBASTIEN , TARASCHEWSKI HORST , MEYER AXEL , WIRTH THIERRY 
Published: July 2008

AbstractProbably half of all animal species exhibit a parasitic lifestyle and numerous parasites have recently expanded their distribution and host ranges due to anthropogenic activities. Here, we report on the population genetic structure of the invasive nematodeAnguillicola crassus,a parasite in freshwater eels, which recently spread from Asia to Europe and North America. Samples were collected from the newly colonized naïve host speciesAnguilla anguilla(Europe) andAnguilla rostrata(North America), and from indigenousAnguilla japonicain Taiwan and Japan. Using seven microsatellite loci and one mitochondrial marker, we show that the parasite's population structure in Europe mirrors the zoogeographic Boreal–Lusitanian break along the English Channel. Both the north‐to‐south decline of nuclear allelic diversity and the loss of private alleles in the same direction are consistent with a significant isolation‐by‐distance pattern based on ρSTvalues. In combination with the specific topology of the distance tree among nematode populations, our data suggest that Europe was invaded only once from Taiwan, and that subsequently, genetic diversity was lost due to random drift. On the contrary, the North American sample shares distinct nuclear and mitochondrial signatures with Japanese specimens. We propose that the genetic structure in Europe was shaped by long‐range anthropogenic eel host transfers in the north and a single dispersal event into the southwest. The genetically distinct Brittany sample at the edge of the Boreal–Lusitanian boundary is indicative of natural dispersal of fish hosts since recruitment occurs naturally there and invertebrate host dissemination is interrupted due to oceanic currents.
The continental record of Ediacaran volcano‐sedimentary successions in southern Brazil and their global implications
Authors: Janikian Liliane , De Almeida Renato Paes , Da Trindade Ricardo Ivan Ferreira , Fragoso‐Cesar Antonio Romalino Santos , D′Agrella‐Filho Manoel Souza , Dantas Elton Luis , Tohver Eric 
Published: July 2008

AbstractThe Ediacaran is one of the most important periods on Earth evolution, including the first appearance of soft‐bodied macrofossils, major climatic changes and a supposed rise in free oxygen. In southernmost Brazil, this period is represented by Camaquã Supergroup, including the Bom Jardim Group and the Acampamento Velho Formation, both of which record continental palaeoenvironmental changes in a more than 5000 m thick stratigraphic succession. Age constraints are given by seven Ar‐Ar and U‐Pb determinations on volcanic rocks, which bracket these units between c. 605 and 574 Ma, revealing the best dated and most continuous documented Ediacaran continental succession to date. Depositional systems evolution supports a Phanerozoic‐type glacial context during the last Neoproterozoic glacial event and presents the Picada das Graças Formation (580 ± 3.6 Ma) as the first dated non‐glacial unit coeval to the Gaskiers Formation.
probeCheck – a central resource for evaluating oligonucleotide probe coverage and specificity
Authors: Loy Alexander , Arnold Roland , Tischler Patrick , Rattei Thomas , Wagner Michael , Horn Matthias 
Published: July 2008

SummaryThe web server probeCheck, freely accessible at http://www.microbial‐ecology.net/probecheck, provides a pivotal forum for rapid specificity and coverage evaluations of probes and primers against selected databases of phylogenetic and functional marker genes. Currently, 24 widely used sequence collections including the Ribosomal Database Project (RDP) II, Greengenes, SILVA and the Functional Gene Pipeline/Repository can be queried. For this purpose, probeCheck integrates a new online version of the popular ARB probe match tool with free energy (ΔG) calculations for each perfectly matched and mismatched probe‐target hybrid, allowing assessment of the theoretical binding stabilities of oligo‐target and non‐target hybrids. For each output sequence, the accession number, the GenBank taxonomy and a link to the respective entry at GenBank, EMBL and, if applicable, the query database are displayed. Filtering options allow customizing results on the output page. In addition, probeCheck is linked with probe match tools of RDP II and Greengenes, NCBI blast, the Oligonucleotide Properties Calculator, the two‐state folding tool of the DINAMelt server and the rRNA‐targeted probe database probeBase. Taken together, these features provide a multifunctional platform with maximal flexibility for the user in the choice of databases and options for the evaluation of published and newly developed probes and primers.
‘I WILL NOT CUT . . . ’: THE OATH THAT DEFINED UROLOGY
Authors: Herr Harry W. 
Published: July 2008

OBJECTIVETo explore different interpretations of the clause embedded in the Hippocratic Oath, prohibiting surgery for stones, and its relevance for urology.METHODSVarious translations of the Oath, from the original Greek edition to historical revisions, were reviewed.RESULTSControversy surrounds different translations and interpretations of the Oath about the practice of lithotomy among ancient healers. The reasons Hippocratic physicians were prohibited from performing lithotomy are several, but the consensus is that untrained physicians pledged not to undertake such a complicated procedure, but to refer their patients to other healers who specialized in that practice.CONCLUSIONThe Hippocratic Oath actually defined, identified and legitimized urology as the first medical speciality.
Exchange Rate Stability, Inflation, and Growth in (South) Eastern and Central Europe
Authors: De Grauwe Paul , Schnabl Gunther 
Published: July 2008

AbstractThe authors analyze the impact of the exchange rate regime on inflation and output in (South) Eastern and Central Europe. For the whole observation period the estimations reveal a significant impact of exchange rate stability on low inflation as well as a highly significant positive impact of exchange stability on real growth. When subdividing the period into a “high‐inflation” period (1994–97) and a “low‐inflation period” (1998–2004), and when removing outliers from the sample, the evidence in favor of a positive association between exchange rate stability and inflation disappears. The association of exchange rate stability with higher real growth remains robust. These findings suggest that membership of the (South) Eastern and Central European countries in the European Monetary Union would have a positive impact on these countries' growth rates.
The Enlargement of the European Union and the Behavior of Real Exchange Rates
Authors: Kutan Ali M. , Zhou Su 
Published: July 2008

AbstractThe authors further investigate the conditional variance and the persistence of real exchange rate (RER) shocks between Germany and some core European Union (EU) members from January, 1973 through 2004. Using data for all EU15 countries, they test whether the enlargement of the Union has reduced the variability and the persistence of RER shocks between Germany and the rest of the members during the 1990s. They also examine the impact of the introduction of the euro on the variance and persistence of real exchange rate shocks. Finally, the authors extend the analysis to the new members who joined in May, 2004. The results have implications for the economic cost of joining the Union, as well as assessing the timing of the newest members to enter the eurozone.
EU Enlargement and Trade Integration: Lessons from a Gravity Model
Authors: Bussière Matthieu , Fidrmuc Jarko , Schnatz Bernd 
Published: July 2008

AbstractThe authors estimate gravity models using a large panel of bilateral trade flows across 61 countries between 1980 and 2003, which are applied as a benchmark for the integration of Central and South Eastern European countries with the euro area. They show that a careful examination of the fixed effects of the model is crucial for the proper interpretation of the results. The results suggest that trade integration between most new EU member states and the euro area is already relatively advanced, while the remaining Central and Eastern European countries have significant scope to strengthen trade links with the euro area.
Exchange Rate Regimes, Foreign Exchange Volatility, and Export Performance in Central and Eastern Europe: Just another Blur Project?
Authors: Égert Balázs , Morales‐Zumaquero Amalia 
Published: July 2008

AbstractThe authors attempt to analyze the direct impact of exchange rate volatility on the export performance of ten Central and Eastern European transition economies, as well as its indirect impact via changes in exchange rate regimes. Not only aggregate but also bilateral and sectoral export flows are studied. To this end, the authors first analyze shifts in exchange rate volatility linked to changes in the exchange rate regimes and, second, they use these changes to construct the dummy variables that they include in their export function. The results suggest that the size and the direction of the impact of forex volatility and of regime changes on exports vary considerably across sectors and countries and that they may be related to specific periods.
Equilibrium Exchange Rates in New EU Members: External Imbalances versus Real Convergence
Authors: Alberola Enrique , Navia Daniel 
Published: July 2008

AbstractIn new EU members, the accumulation of net foreign liabilities has gone hand‐in‐hand with real exchange rate appreciations, contrary to intuition. This may be due to the induced effect that capital inflows on productivity and competitiveness (Balassa‐Samuelson effect). An extended empirical model comprising relative productivity and net foreign assets is well‐suited to capture this indirect, opposite effect of liabilities accumulation on the equilibrium exchange rates for the three largest economies: Poland, Hungary and Czech Republic. The model makes it possible to estimate equilibrium exchange rates and misalignments. Going forward, sustaining high productivity growth will be essential to ensure a smooth transition towards euro membership.