bluuebunny/crossref_metadata_2025_split huggingface dataset:
Opposite Effects of Tor1 and Tor2 on Nitrogen Starvation Responses in Fission Yeast
Authors: Weisman Ronit , Roitburg Irina , Schonbrun Miriam , Harari Rona , Kupiec Martin 
Published: December 2006

Abstract
The TOR protein kinases exhibit a conserved role in regulating cellular growth and proliferation. In the fission yeast two TOR homologs are present. tor1+ is required for starvation and stress responses, while tor2+ is essential. We report here that Tor2 depleted cells show a phenotype very similar to that of wild-type cells starved for nitrogen, including arrest at the G1 phase of the cell cycle, induction of nitrogen-starvation-specific genes, and entrance into the sexual development pathway. The phenotype of tor2 mutants is in a striking contrast to the failure of tor1 mutants to initiate sexual development or arrest in G1 under nitrogen starvation conditions. Tsc1 and Tsc2, the genes mutated in the human tuberous sclerosis complex syndrome, negatively regulate the mammalian TOR via inactivation of the GTPase Rheb. We analyzed the genetic relationship between the two TOR genes and the Schizosaccharomyces pombe orthologs of TSC1, TSC2, and Rheb. Our data suggest that like in higher eukaryotes, the Tsc1–2 complex negatively regulates Tor2. In contrast, the Tsc1–2 complex and Tor1 appear to work in parallel, both positively regulating amino acid uptake through the control of expression of amino acid permeases. Additionally, either Tsc1/2 or Tor1 are required for growth on a poor nitrogen source such as proline. Mutants lacking Tsc1 or Tsc2 are highly sensitive to rapamycin under poor nitrogen conditions, suggesting that the function of Tor1 under such conditions is sensitive to rapamycin. We discuss the complex genetic interactions between tor1+, tor2+, and tsc1/2+ and the implications for rapamycin sensitivity in tsc1 or tsc2 mutants.
Misexpression Screen in Drosophila melanogaster Aiming to Reveal Novel Factors Involved in Formation of Body Parts
Authors: Grieder Nicole C , Charlafti Ilias , Kloter Urs , Jäckle Herbert , Schäfer Ulrich , Gehring Walter J 
Published: December 2006

Abstract
To identify novel factors that lead a fly imaginal disc to adopt its developmental fate, we carried out a modular dominant misexpression screen in imaginal discs. We have identified two factors that appear to change the fate of the respective body structure and appear to lead to the transformation of a body part. In one mutant line, notum tissue, normally derived from wing imaginal tissue, formed close to the site of the sternopleural bristles, which are leg disc derivatives. In the other line, the arista is transformed into a tubular structure, resembling an abnormal leg. We found that ectopic expression of abrupt was responsible for this potential transformation of the arista.
In Vivo Construction of Transgenes in Drosophila
Authors: Takeuchi Hajime , Georgiev Oleg , Fetchko Michael , Kappeler Michael , Schaffner Walter , Egli Dieter 
Published: December 2006

Abstract
Transgenic flies are generated by transposon-mediated transformation. A drawback of this approach is the size limit of transposable elements. Here, we propose a novel method that allows the extension of transgenes in vivo. This method is based on an incomplete transgene that has been constructed in vitro and integrated into the Drosophila genome by conventional transgenesis. The incomplete transgene contains two short stretches of DNA homologous to the 5′- and 3′-ends of a larger DNA segment of interest. Between the short stretches of homology an I-SceI recognition site is located. Once activated, I-SceI endonuclease introduces a DNA double-strand break, which triggers ectopic recombination between the stretches of homology and the endogenous locus. Through gap repair, the transgene obtains the complete region of interest in vivo. Our results show that this method is effective for copying up to 28 kb of genomic DNA into the transgene, thereby eliminating the technical difficulties associated with the in vitro construction of large transgenes and extending the size limits of current transgenesis protocols. In general, this method may be a useful technique for genetic engineering of eukaryotic model organisms.
Contribution of Trf4/5 and the Nuclear Exosome to Genome Stability Through Regulation of Histone mRNA Levels in Saccharomyces cerevisiae
Authors: Reis Clara C , Campbell Judith L 
Published: December 2006

Abstract
Balanced levels of histones are crucial for chromosome stability, and one major component of this control regulates histone mRNA amounts. The Saccharomyces cerevisiae poly(A) polymerases Trf4 and Trf5 are involved in a quality control mechanism that mediates polyadenylation and consequent degradation of various RNA species by the nuclear exosome. None of the known RNA targets, however, explains the fact that trf mutants have specific cell cycle defects consistent with a role in maintaining genome stability. Here, we investigate the role of Trf4/5 in regulation of histone mRNA levels. We show that loss of Trf4 and Trf5, or of Rrp6, a component of the nuclear exosome, results in elevated levels of transcripts encoding DNA replication-dependent histones. Suggesting that increased histone levels account for the phenotypes of trf mutants, we find that TRF4 shows synthetic genetic interactions with genes that negatively regulate histone levels, including RAD53. Moreover, synthetic lethality of trf4Δ rad53Δ is rescued by reducing histone levels whereas overproduction of histones is deleterious to trf's and rrp6Δ mutants. These results identify TRF4, TRF5, and RRP6 as new players in the regulation of histone mRNA levels in yeast. To our knowledge, the histone transcripts are the first mRNAs that are upregulated in Trf mutants.
Exploring Strategies for Protein Trapping in Drosophila
Authors: Quiñones-Coello Ana T , Petrella Lisa N , Ayers Kathleen , Melillo Anthony , Mazzalupo Stacy , Hudson Andrew M , Wang Shu , Castiblanco Claudia , Buszczak Michael , Hoskins Roger A , Cooley Lynn 
Published: December 2006

AbstractThe use of fluorescent protein tags has had a huge impact on cell biological studies in virtually every experimental system. Incorporation of coding sequence for fluorescent proteins such as green fluorescent protein (GFP) into genes at their endogenous chromosomal position is especially useful for generating GFP-fusion proteins that provide accurate cellular and subcellular expression data. We tested modifications of a transposon-based protein trap screening procedure in Drosophila to optimize the rate of recovering useful protein traps and their analysis. Transposons carrying the GFP-coding sequence flanked by splice acceptor and donor sequences were mobilized, and new insertions that resulted in production of GFP were captured using an automated embryo sorter. Individual stocks were established, GFP expression was analyzed during oogenesis, and insertion sites were determined by sequencing genomic DNA flanking the insertions. The resulting collection includes lines with protein traps in which GFP was spliced into mRNAs and embedded within endogenous proteins or enhancer traps in which GFP expression depended on splicing into transposon-derived RNA. We report a total of 335 genes associated with protein or enhancer traps and a web-accessible database for viewing molecular information and expression data for these genes.
Epigenetic Modifications of Distinct Sequences of thep1Regulatory Gene Specify Tissue-Specific Expression Patterns in Maize
Authors: Sekhon Rajandeep S , Peterson Thomas , Chopra Surinder 
Published: December 2006

AbstractTandemly repeated endogenous genes are common in plants, but their transcriptional regulation is not well characterized. In maize, the P1-wr allele of pericarp color1 is composed of multiple copies arranged in a head-to-tail fashion. P1-wr confers a white kernel pericarp and red cob glume pigment phenotype that is stably inherited over generations. To understand the molecular mechanisms that regulate tissue-specific expression of P1-wr, we have characterized P1-wr*, a spontaneous loss-of-function epimutation that shows a white kernel pericarp and white cob glume phenotype. As compared to its progenitor P1-wr, the P1-wr* is hypermethylated in exon 1 and intron 2 regions. In the presence of the epigenetic modifier Ufo1 (Unstable factor for orange1), P1-wr* plants exhibit a range of cob glume pigmentation whereas pericarps remain colorless. In these plants, the level of cob pigmentation directly correlates with the degree of DNA demethylation in the intron 2 region of p1. Further, genomic bisulfite sequencing indicates that a 168-bp region of intron 2 is significantly hypomethylated in both CG and CNG context in P1-wr* Ufo1 plants. Interestingly, P1-wr* Ufo1 plants did not show any methylation change in a distal enhancer region that has previously been implicated in Ufo1-induced gain of pericarp pigmentation of the P1-wr allele. These results suggest that distinct regulatory sequences in the P1-wr promoter and intron 2 regions can undergo independent epigenetic modifications to generate tissue-specific expression patterns.
The Alternative Pathway of Glutathione Degradation Is Mediated by a Novel Protein Complex Involving Three New Genes in Saccharomyces cerevisiae
Authors: Ganguli Dwaipayan , Kumar Chitranshu , Bachhawat Anand Kumar 
Published: December 2006

Abstract
Glutathione (GSH), l-γ-glutamyl-l-cysteinyl-glycine, is the major low-molecular-weight thiol compound present in almost all eukaryotic cells. GSH degradation proceeds through the γ-glutamyl cycle that is initiated, in all organisms, by the action of γ-glutamyl transpeptidase. A novel pathway for the degradation of GSH that requires the participation of three previously uncharacterized genes is described in the yeast Saccharomyces cerevisiae. These genes have been named DUG1 (YFR044c), DUG2 (YBR281c), and DUG3 (YNL191w) (defective in utilization of glutathione). Although dipeptides and tripeptides with a normal peptide bond such as cys-gly or glu-cys-gly required the presence of only a functional DUG1 gene that encoded a protein belonging to the M20A metallohydrolase family, the presence of an unusual peptide bond such as in the dipeptide, γ-glu-cys, or in GSH, required the participation of the DUG2 and DUG3 gene products as well. The DUG2 gene encodes a protein with a peptidase domain and a large WD40 repeat region, while the DUG3 gene encoded a protein with a glutamine amidotransferase domain. The Dug1p, Dug2p, and Dug3p proteins were found to form a degradosomal complex through Dug1p–Dug2p and Dug2p–Dug3p interactions. A model is proposed for the functioning of the Dug1p/Dug2p/Dug3p proteins as a specific GSH degradosomal complex.
Inheritance of Gynandromorphism in the Parasitic Wasp Nasonia vitripennis
Authors: Kamping Albert , Katju Vaishali , Beukeboom Leo W , Werren John H 
Published: December 2006

Abstract
The parasitic wasp Nasonia vitripennis has haplo-diploid sex determination. Males develop from unfertilized eggs and are haploid, whereas females develop from fertilized eggs and are diploid. Females and males can be easily distinguished by their morphology. A strain that produces individuals with both male and female features (gynandromorphs) is studied. We provide data on female/male patterning within and between individuals, on environmental effects influencing the occurrence of gynandromorphism, and on its pattern of inheritance. A clear anterior/posterior pattern of feminization is evident in gynandromorphic individuals that developed from unfertilized haploid eggs. The proportion of gynandromorphic individuals can be increased by exposing the mothers to high temperature and also by exposing embryos at early stages of development. Selection for increased gynandromorph frequency was successful. Backcross and introgression experiments showed that a combination of a nuclear and a heritable cytoplasmic component causes gynandromorphism. Analyses of reciprocal F2 and F3 progeny indicate a maternal effect locus (gyn1) that maps to chromosome IV. Coupled with previous studies, our results are consistent with a N. vitripennis sex determination involving a maternal/zygotic balance system and/or maternal imprinting. Genetics and temperature effects suggest a temperature-sensitive mutation of a maternally produced masculinizing product that acts during a critical period in early embryogenesis.
Histone H3 Lysine 36 Methylation Antagonizes Silencing in Saccharomyces cerevisiae Independently of the Rpd3S Histone Deacetylase Complex
Authors: Tompa Rachel , Madhani Hiten D 
Published: December 2006

Abstract
In yeast, methylation of histone H3 on lysine 36 (H3-K36) is catalyzed by the NSD1 leukemia oncoprotein homolog Set2. The histone deacetylase complex Rpd3S is recruited to chromatin via binding of the chromodomain protein Eaf3 to methylated H3-K36 to prevent erroneous transcription initiation. Here we identify a distinct function for H3-K36 methylation. We used random mutagenesis of histones H3 and H4 followed by a reporter-based screen to identify residues necessary to prevent the ectopic spread of silencing from the silent mating-type locus HMRa into flanking euchromatin. Mutations in H3-K36 or deletion of SET2 caused ectopic silencing of a heterochromatin-adjacent reporter. Transcriptional profiling revealed that telomere-proximal genes are enriched for those that display decreased expression in a set2Δ strain. Deletion of SIR4 rescued the expression defect of 26 of 37 telomere-proximal genes with reduced expression in set2Δ cells, implying that H3-K36 methylation prevents the spread of telomeric silencing. Indeed, Sir3 spreads from heterochromatin into neighboring euchromatin in set2Δ cells. Furthermore, genetic experiments demonstrated that cells lacking the Rpd3S-specific subunits Eaf3 or Rco1 did not display the anti-silencing phenotype of mutations in SET2 or H3-K36. Thus, antagonism of silencing is independent of the only known effector of this conserved histone modification.
Identification of Genes That Interact With Drosophila liquid facets
Authors: Eun Suk Ho , Lea Kristi , Overstreet Erin , Stevens Samuel , Lee Ji-Hoon , Fischer Janice A 
Published: December 2006

Abstract
We have performed mutagenesis screens of the Drosophila X chromosome and the autosomes for dominant enhancers of the rough eye resulting from overexpression of liquid facets. The liquid facets gene encodes the homolog of vertebrate endocytic Epsin, an endocytic adapter protein. In Drosophila, Liquid facets is a core component of the Notch signaling pathway required in the signaling cells for ligand endocytosis and signaling. Why ligand internalization by the signaling cells is essential for signaling is a mystery. The requirement for Liquid facets is a hint at the answer, and the genes identified in this screen provide further clues. Mutant alleles of clathrin heavy chain, Rala, split ends, and auxilin were identified as enhancers. We describe the mutant alleles and mutant phenotypes of Rala and aux. We discuss the relevance of all of these genetic interactions to the function of Liquid facets in Notch signaling.
Gas Process Displacement Efficiency Comparisons on a Carbonate Reservoir
Authors: Egermann P. , Robin M. , Lombard J.-M. , Modavi A. , Kalam M. Z. 
Published: December 2006

Summary
Secondary- and tertiary-recovery processes based on gas injection can extend the life of waterflooded reservoirs by maximizing the oil recovery. However, the injection strategy needs to be studied carefully to optimize the overall sweep efficiency. In particular, the impact of possible water blocking on the recovery has to be addressed. For that purpose, a series of experiments was performed under reservoir conditions on a carbonate rock type to compare the displacement efficiencies of a secondary gas injection, a tertiary gas injection, and a simultaneous water-alternating-gas (SWAG) injection.
The experiments were carried out on composite cores consisting of several carefully selected reservoir core plugs of the chosen rock type. The operating pressure was lower than the minimum miscible pressure (MMP) and reflected the current reservoir pressure. Phase exchanges were monitored continually during the hydrocarbon recovery, including the chromatographic analysis of the produced gas.
The final oil recovery resulting from the three types of experiments was very good [approximately 90% original oil in place (OOIP) at surface conditions after 6 pore-volume (PV) injection] and quite similar within the expected experimental error, regardless of the sequence of gas injection. The low remaining oil saturation (ROS) values observed were consistent with competing processes of both viscous displacement of oil by gas and phase exchanges occurring between oil and gas. Because of the nature of the injected gas (rich gas from the first separation stage), a condensing/vaporizing process had to be considered. The SWAG injection speeds up the oil recovery by mobility control of the water phase. This enhances the sweep efficiency by viscous drive. A water-blocking effect was found to be negligible because it could be anticipated due to wettability consideration.
The influence of the fluid description (equation of state, or EOS) and the three-phase relative permeability model on the simulation results was studied. An excellent agreement between simulation and production data was obtained with both gas/oil relative permeability data measured at ambient conditions on a restored composite core and an appropriate EOS (with seven pseudos). The condensing/vaporizing process that strips the intermediate compounds from the oil phase to the gas phase was properly taken into account with this appropriate EOS. The influence of the three-phase permeability model (either "geometrical construction" or Stone1) on the results was found to be small.
Insuring the Portfolio Against Large Project Failure
Authors: DuBois James R. , Quarles Andrew I. 
Published: December 2006

Summary
There is a growing body of literature in our industry that addresses the use of portfolio-management techniques to find "optimum" mixes of projects that meet company goals while managing risk. These investigations usually start by describing "risk" in some manner, then proceed to illustrate how combinations of properties can be chosen that minimize this risk function subject to the other goals of the company. The probabilities of meeting individual metric targets in discrete time frames also can and should be quantified.
This type of analysis is valid and useful, and it forms the backbone of project portfolio management. However, when dealing with risk and probability concepts, it is easy to lose sight of the fact that specific events will occur in time and that the portfolio must include enough flexibility to allow reaction to and recovery from these events.
Specifically, acceptable portfolio results may depend on a small number of projects performing at a certain level. Because the chance of these important projects not performing at this level may be relatively small, the risk is deemed "acceptable." If one of the projects subsequently fails to perform, what was once "acceptable risk" can become an exercise in salvaging a year or even saving a company.
This paper shows how portfolio-management techniques can be used to plan a portfolio robust enough to recover from the potential failure of a significant project. These techniques can lead us to make investment choices today that might not be obvious if projects are evaluated solely with their expected values; those choices, if made judiciously, can provide insurance against a possible future downside.
Portfolio analysis is a powerful technique, with applications far beyond the standard risk/reward exercise. The examples presented demonstrate how this analysis can be used to provide insight into the practical business questions that truly concern company management.
Modeling Original Water Saturation in the Transition Zone of a Carbonate Oil Reservoir
Authors: Ghedan Shawket G. , Thiebot Bertrand M. , Boyd Douglas A. 
Published: December 2006

Summary
Accurately modeling water-saturation variation in transition zones is important to reservoir simulation for predicting recoverable oil and guiding field-development plans. The large transition zone of a heterogeneous Middle East reservoir was challenging to model. Core-calibrated, log-derived water saturations were used to generate saturation-height-function groups for nine reservoir-rock types. To match the large span of log water saturation (Sw)in the transition zone from the free-water level (FWL) to minimum Sw high in the oil column, three saturation-height functions per rock type (RT) were developed, one each for the low-, medium-, and high-porosity range.
Though developed on a different scale from the simulationmodel cells, the saturation profiles generated are a good statistical match to the wireline-log-interpreted Sw, and bulk volume of water (BVW) and fluid volumetrics agree with the geological model. RT-guided saturation-height functions proved a good method for modeling water saturation in the simulation model.
The technique emphasizes the importance of oil/brine capillary pressures measured under reservoir conditions and of collecting an adequate number of Archie saturation and cementation exponents to reduce uncertainties in well-log interpretation.
Oil- and Water-Content Measurements in Bitumen Ore and Froth Samples Using Low-Field NMR
Authors: Bryan J. , Mai A. , Hum F. , Kantzas A. 
Published: December 2006

Summary
Low-field nuclear magnetic resonance (NMR) relaxometry has been used successfully to perform estimates of oil and water content in unconsolidated oil-sand samples. This work has intriguing applications in the oil-sands mining and processing industry, in the areas of ore and froth characterization. Studies have been performed on a database of ore and froth samples from the Athabasca region in northern Alberta, Canada. In this paper, new automated algorithms are presented that predict the oil- and water-weight content of oil-sand ores and froths.
Suites of real and synthetic samples of bitumen, water, clay, and sand have also been used to investigate the physical interactions of the different parameters on the NMR spectra. Preliminary observations regarding spectral properties indicate that it may be possible in the future to estimate the amount of clay in the samples, based upon shifts in the NMR spectra. NMR estimates of oil and water content are fairly accurate, thus enhancing the possibility of using NMR for oil-sands development and in the oil-sands mining industry.
Acetaldehyde
Authors: Eckert Marc , Fleischmann Gerald , Jira Reinhard , Bolt Hermann M. , Golka Klaus 
Published: December 2006

AbstractThe article contains sections titled:1.Introduction2.Physical Properties3.Chemical Properties and Uses3.1.Addition Reactions3.2.Derivatives of Aldol Addition3.3.Reaction with Nitrogen Compounds3.4.Oxidation3.5.Reduction3.6.Miscellaneous Reactions3.7.Consumption4.Production4.1.Production from Ethanol4.2.Production from Acetylene4.3.Production from Ethylene4.3.1.Direct Oxidation of Ethylene4.3.2.Acetaldehyde as Byproduct4.3.3.Isomerization of Ethylene Oxide4.4.Production from C1Sources4.5.Production from Hydrocarbons5.Quality and Analysis6.Storage and Transportation6.1.Storage6.2.Transportation6.3.Other Regulations7.Economic Aspects8.Polymers of Acetaldehyde8.1.Paraldehyde8.2.Metaldehyde8.3.Polyacetaldehyde9.Toxicology and Occupational Health