bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Peroxiredoxin and Glutathione Peroxidase Families in Chlamydomonas reinhardtii
Authors: Dayer Régine , Fischer Beat B , Eggen Rik I L , Lemaire Stéphane D 
Published: May 2008

Abstract
Thiol/selenol peroxidases are ubiquitous nonheme peroxidases. They are divided into two major subfamilies: peroxiredoxins (PRXs) and glutathione peroxidases (GPXs). PRXs are present in diverse subcellular compartments and divided into four types: 2-cys PRX, 1-cys PRX, PRX-Q, and type II PRX (PRXII). In mammals, most GPXs are selenoenzymes containing a highly reactive selenocysteine in their active site while yeast and land plants are devoid of selenoproteins but contain nonselenium GPXs. The presence of a chloroplastic 2-cys PRX, a nonselenium GPX, and two selenium-dependent GPXs has been reported in the unicellular green alga Chlamydomonas reinhardtii. The availability of the Chlamydomonas genome sequence offers the opportunity to complete our knowledge on thiol/selenol peroxidases in this organism. In this article, Chlamydomonas PRX and GPX families are presented and compared to their counterparts in Arabidopsis, human, yeast, and Synechocystis sp. A summary of the current knowledge on each family of peroxidases, especially in photosynthetic organisms, phylogenetic analyses, and investigations of the putative subcellular localization of each protein and its relative expression level, on the basis of EST data, are presented. We show that Chlamydomonas PRX and GPX families share some similarities with other photosynthetic organisms but also with human cells. The data are discussed in view of recent results suggesting that these enzymes are important scavengers of reactive oxygen species (ROS) and reactive nitrogen species (RNS) but also play a role in ROS signaling.
Genome-Based Analysis of Chlamydomonas reinhardtii Exoribonucleases and Poly(A) Polymerases Predicts Unexpected Organellar and Exosomal Features
Authors: Zimmer Sara L , Fei Zhangjun , Stern David B 
Published: May 2008

Abstract
Enzymes from several gene families modify RNA molecules at their extremities. These reactions occur in several cellular compartments and affect every class of RNA. To assess the diversity of a subclass of these enzymes, we searched Chlamydomonas for open reading frames (ORFs) potentially encoding exoribonucleases, poly(A) polymerases, and proteins known to associate with and/or regulate them. The ORFs were further analyzed for indications of protein localization to the nucleus, cytosol, mitochondrion, and/or chloroplast. By comparing predicted proteins with homologs in Arabidopsis and yeast, we derived several tentative conclusions regarding RNA 5′- and 3′-end metabolism in Chlamydomonas. First, the alga possesses only one each of the following likely organellar enzymes: polynucleotide phosphorylase, hydrolytic exoribonuclease, poly(A) polymerase, and CCA transferase, a surprisingly small complement. Second, although the core of the nuclear/cytosolic exosome decay complex is well conserved, neither nucleus-specific activators nor the cytosolic exosome activators are present. Finally, our discovery of nine noncanonical poly(A) polymerases, a divergent family retaining the catalytic domains of conventional poly(A) polymerases, leads to the hypothesis that polyadenylation may play an especially important regulatory role throughout the Chlamydomonas cell, stabilizing some transcripts and targeting degradation machinery to others.
Variation and Evolution of Male Sex Combs in Drosophila: Nature of Selection Response and Theories of Genetic Variation for Sexual Traits
Authors: Ahuja Abha , Singh Rama S 
Published: May 2008

Abstract
We investigated the genetic architecture of variation in male sex comb bristle number, a rapidly evolving secondary sexual character of Drosophila. Twenty-four generations of divergent artificial selection for sex comb bristle number in a heterogeneous population of Drosophila melanogaster resulted in a significant response that was more pronounced in the direction of low bristle numbers. We observed a strong positive correlated response to selection in the corresponding female transverse bristle row. The correlated response in male abdominal and sternopleural bristle numbers, on the other hand, did not follow the same pattern as sex comb bristle number differences between selection lines. Relaxation-of-selection experiments along with mate choice and fecundity assays using the selection lines developed demonstrated the action of stabilizing selection on sex comb bristle number. Our results show (1) substantial genetic variation underlying sex comb bristle number variation; (2) a weak relationship between the sex comb and developmentally related, non-sex bristle systems; and (3) that sexual selection may be a driving force in sex comb evolution, indicating the potential of sex combs to diversify rapidly during population differentiation and speciation. We discuss the implications of these results for theories of genetic variation in display and nondisplay male sex traits.
Saccharomyces cerevisiae Yta7 Regulates Histone Gene Expression
Authors: Gradolatto Angeline , Rogers Richard S , Lavender Heather , Taverna Sean D , Allis C David , Aitchison John D , Tackett Alan J 
Published: May 2008

Abstract
The Saccharomyces cerevisiae Yta7 protein is a component of a nucleosome bound protein complex that maintains distinct transcriptional zones of chromatin. We previously found that one protein copurifying with Yta7 is the yFACT member Spt16. Epistasis analyses revealed a link between Yta7, Spt16, and other previously identified members of the histone regulatory pathway. In concurrence, Yta7 was found to regulate histone gene transcription in a cell-cycle-dependent manner. Association at the histone gene loci appeared to occur through binding of the bromodomain-like region of Yta7 with the N-terminal tail of histone H3. Our work suggests a mechanism in which Yta7 is localized to chromatin to establish regions of transcriptional silencing, and that one facet of this cellular mechanism is to modulate transcription of histone genes.
Functional Characterization of the Drosophila Hmt4-20/Suv4-20 Histone Methyltransferase
Authors: Sakaguchi Ayako , Karachentsev Dmitry , Seth-Pasricha Mansha , Druzhinina Marina , Steward Ruth 
Published: May 2008

AbstractDi- and trimethylation of histone H4 lysine20 (H4K20) are thought to play an important role in controlling gene expression in vertebrates and in Drosophila. By inducing a null mutation in Drosophila Suv4-20, we show that it encodes the histone H4 lysine20 di- and trimethyltransferase. In Suv4-20 mutants, the H4K20 di- and trimethyl marks are strongly reduced or absent, and the monomethyl mark is significantly increased. We find that even with this biochemical function, Suv4-20 is not required for survival and does not control position-effect variegation (PEV).
Identification of New Quantitative Trait Loci (Other Than the PRNP Gene) Modulating the Scrapie Incubation Period in Sheep
Authors: Moreno C R , Cosseddu G M , Schibler L , Roig A , Moazami-Goudarzi K , Andreoletti O , Eychenne F , Lajous D , Schelcher F , Cribiu E P , Laurent P , Vaiman D , Elsen J M 
Published: May 2008

Abstract
Although susceptibility to scrapie is largely controlled by the PRNP gene, we have searched for additional genomic regions that affect scrapie incubation time in sheep, using two half-sib families with a susceptible PRNP genotype and naturally infected by scrapie. Quantitative trait loci were detected on OAR6 and OAR18.
Unique Features of Nuclear mRNA Poly(A) Signals and Alternative Polyadenylation in Chlamydomonas reinhardtii
Authors: Shen Yingjia , Liu Yuansheng , Liu Lin , Liang Chun , Li Qingshun Q 
Published: May 2008

Abstract
To understand nuclear mRNA polyadenylation mechanisms in the model alga Chlamydomonas reinhardtii, we generated a data set of 16,952 in silico-verified poly(A) sites from EST sequencing traces based on Chlamydomonas Genome Assembly v.3.1. Analysis of this data set revealed a unique and complex polyadenylation signal profile that is setting Chlamydomonas apart from other organisms. In contrast to the high-AU content in the 3′-UTRs of other organisms, Chlamydomonas shows a high-guanylate content that transits to high-cytidylate around the poly(A) site. The average length of the 3′-UTR is 595 nucleotides (nt), significantly longer than that of Arabidopsis and rice. The dominant poly(A) signal, UGUAA, was found in 52% of the near-upstream elements, and its occurrence may be positively correlated with higher gene expression levels. The UGUAA signal also exists in Arabidopsis and in some mammalian genes but mainly in the far-upstream elements, suggesting a shift in function. The C-rich region after poly(A) sites with unique signal elements is a characteristic downstream element that is lacking in higher plants. We also found a high level of alternative polyadenylation in the Chlamydomonas genome, with a range of up to 33% of the 4057 genes analyzed having at least two unique poly(A) sites and ∼1% of these genes having poly(A) sites residing in predicted coding sequences, introns, and 5′-UTRs. These potentially contribute to transcriptome diversity and gene expression regulation.
Aqueous toxicity and food chain transfer of quantum dots™ in freshwater algae andCeriodaphnia dubia
Authors: Bouldin Jennifer L , Ingle Taylor M , Sengupta Anindita , Alexander Regina , Hannigan Robyn E , Buchanan Roger A 
Published: May 2008

AbstractInnovative research and diagnostic techniques for biological testing have advanced during recent years because of the development of semiconductor nanocrystals. Although these commercially available, fluorescent nanocrystals have a protective organic coating, the inner core contains cadmium and selenium. Because these metals have the potential for detrimental environmental effects, concerns have been raised over our lack of understanding about the environmental fate of these products. U.S. Environmental Protection Agency test protocol and fluorescence microscopy were used to determine the fate and effect of quantum dots (QDs; Qdot® 545 ITK™ Carboxyl Quantum Dots [Fisher Scientific, Fisher part Q21391MP; Invitrogen Molecular Probes, Eugene, OR, USA]) using standard aquatic test organisms. No lethality was measured following 48-h exposure of Ceriodaphnia dubia to QD suspensions as high as 110 ppb, but the 96-h median lethal concentration to Pseudokirchneriella subcapitata was measured at 37.1 ppb. Transfer of QDs from dosed algae to C. dubia was verified with fluorescence microscopy. These results indicate that coatings present on nanocrystals provide protection from metal toxicity during laboratory exposures but that the transfer of core metals from intact nanocrystals may occur at levels well above toxic threshold values, indicating the potential exposure of higher trophic levels. Studies regarding the fate and effects of nanoparticles can be incorporated into models for predictive toxicology of these emerging contaminants.
On Instability in Gas Lift Wells and Schemes for Stabilization by Automatic Control
Authors: Eikrem Gisle Otto , Aamo Ole Morten , Foss Bjarne A. 
Published: May 2008

Summary
In this paper, we present a simple nonlinear dynamic model that is shown to capture the essential dynamics of the casing-heading instability in gas lift wells despite the complex nature of two-phase flow. Using the model, stability maps are generated showing regions of stable and unstable settings for the production valve governing the flow of produced oil and gas from the tubing. Optimal steady-state production is shown to lie well within the unstable region, corresponding to an oil-production rate that cannot be sustained without automatic control. Three simple control structures are suggested that successfully stabilize the casing-heading instability in simulations, and more importantly in laboratory experiments.
Effect of Formation Modulus Contrast on Hydraulic Fracture Height Containment
Authors: Gu Hongren , Siebrits Eduard 
Published: May 2008

Summary
Much study has been conducted on the effect of formation Young's modulus and in situ stress on hydraulic fracture height containment in layered formations. It has been well documented that in situ stress contrast is the dominant parameter controlling fracture height growth, and that Young's modulus contrast is less important. However, a recent study pointed out that modulus contrast can have significant implications on fracture geometry and proppant placement (Smith et al. 2001). To expand on this topic, we consider the combined effects of modulus contrast and in situ stress contrast on fracture geometry. A pseudo 3D (P3D) hydraulic fracture simulator with a rigorous layered modulus formulation is used in this study. The fracture height calculated based on uniform modulus vs. layered modulus, under the same in situ stress contrast conditions, is compared.
The results are analyzed and explained, based on fracture mechanics fundamentals as well as the coupled fluid pressure effect in hydraulic fracturing. One important finding is that low-modulus layers can also contain fracture height. The results from this study can be applied to hydraulic fracturing treatments in formations with moderate to significant modulus contrast. The mechanisms studied in this work can also partially explain some recent results from microseismic or tiltmeter mapping that show more fracture height containment than that predicted by commonly used P3D hydraulic fracturing simulators based on averaged modulus.
Field-Development Case Study: Production Optimization Through Continuous Multidisciplinary Reservoir and Production Monitoring
Authors: Ruiz Hector , Poettmann Phil , Kryuchkova Tatiana , Igoshkin Vladimir , Edelman Inna , Kalita Nik , Voicu Bogdan 
Published: May 2008

Summary
This paper presents a field-development case study of a low-permeability turbidite reservoir in Russia. The giant Priobskoye field contains 30°API crude in laminated sandstones of 0.1 to 20 md at a depth of approximately 2,500 m. The complex geology, lack of reservoir information and lack of technology availability caused a 20-year gap between discovery and development.
The initial pilot development was halted after poor drilling success, thus the operator invested in 3D-seismic acquisition and an integrated, multidisciplinary reservoir modeling and simulation effort. The subsequent development was based on oriented water-flooding patterns and massive hydraulic fracturing, together with an artificial-lift system equipped with permanent pressure and rate monitoring for evaluation and real-time production enhancement.
The optimization of operational practices and introduction of fit-for-purpose technologies enabled a production increase from an intermittent hundreds of BOPD to more than 75,000 BOPD in a period of 3.5 years. The exploitation strategy of this pilot area demonstrated commercially sustainable production from the reservoir and will form the basis for full field development.
High-Viscosity-Yield Acid Systems for High-Temperature Stimulation
Authors: Welton Thomas D. , Van Domelen Mary S. 
Published: May 2008

Summary
This paper discusses the development of a unique in-situ crosslinkable acid system that uses a blend of hydrochloric acid (Hcl)/formic acid as the base acid and a synthetic polymer gelling agent. The ability to in-situ crosslink an organic acid blend is novel. In addition, an unexpected result of the fluid development was the discovery of its unique rheological properties.
Historically, both gelled and in-situ-crosslinked acids have been used for fluid-loss control during fracture acidizing and for diversion in matrix treatments in carbonate formations. Various synthetic polymers are used to gel the acid. Past research indicates that ~20 cp base-gel viscosity is required as the first step in fluid-loss control. In-situ crosslinking allows very high viscosities to be generated as the acid spends. The crosslinked gel creates a permeability barrier and subsequent fluid stages are diverted to other sections of the zone. When the acid fully spends, the gel breaks, giving a low-viscosity fluid.
HCl is the most common base acid used for carbonate stimulation. Combinations of HCl and organic acids have been used because of their high dissolving power and relatively low rates of corrosion at elevated temperatures. In extreme cases, combinations of organic acids are used. While HCl/formic-acid blends have been used in the past, the unique rheological properties of these blends have not been fully explored.
The chemistry and rheology of gelled and in-situ crosslinked HCl/formic-acid blends equivalent to 28% HCl will be described and compared with traditional gelled acid and in-situ crosslinked acid.
Analysis of Possible Applications of Dual ESPs—A Reservoir-Engineering Perspective
Authors: Davies D. R. , Narayanasamy R. , Kristensen B. , Somerville J. M. 
Published: May 2008

Summary
Relatively few field installations of a dual-electric submersible-pump (DESP) completion have been reported. In general, the purpose of the second pump was either to increase the pumping capacity, or to act as a backup to improve the reliability of the pumping system. However, DESPs potentially can address a much wider range of reservoir management challenges. This paper will analyze the performance of a DESP in a range of reservoir scenarios. It will show how DESP performance can be modeled by use of commercially available, coupled, well-performance and reservoir-simulation tools.
Four DESP applications were analyzed. Where possible, the robustness of the numerical-modeling results will be compared with analytical predictions. DESPs gave improved oil production and recovery in reservoirs with strong aquifer support and became progressively more attractive in a layered-reservoir scenario as the pressure difference between the production zones increased. However, while DESPs had no significant advantages in a long, horizontal well placed in a homogeneous reservoir, they can increase recovery in a tilted, layered reservoir. A slim, deepwater well completed with a lower-capacity downhole pump and a larger (multiwell) seabed booster pump was shown to be a potentially attractive solution for some reservoir developments.
This work provides a comparison of the drivers for the choice of a single electric submersible pump (SESP) and a DESP in the scenarios studied. It illustrates a modeling methodology and provides DESP-selection guidelines, thus aiding the increased application of this technology.
Altered Calcium Homeostasis Does Not Explain the Contractile Deficit of Diabetic Cardiomyopathy
Authors: Zhang Lin , Cannell Mark B. , Phillips Anthony R.J. , Cooper Garth J.S. , Ward Marie-Louise 
Published: May 2008

OBJECTIVE—This study examines the extent to which the contractile deficit of diabetic cardiomyopathy is due to altered Ca2+ homeostasis.
RESEARCH DESIGN AND METHODS—Measurements of isometric force and intracellular calcium ([Ca2+]i, using fura-2/AM) were made in left ventricular (LV) trabeculae from rats with streptozotocin-induced diabetes and age-matched siblings.
RESULTS—At 1.5 mmol/l [Ca2+]o, 37°C, and 5-Hz stimulation frequency, peak stress was depressed in diabetic rats (10 ± 1 vs. 17 ± 2 mN/mm2 in controls; P &lt; 0.05) with a slower time to peak stress (77 ± 3 vs. 67 ± 2 ms; P &lt; 0.01) and time to 90% relaxation (76 ± 7 vs. 56 ± 3 ms; P &lt; 0.05). No difference was found between groups for either resting or peak Ca2+, but the Ca2+ transient was slower in time to peak (39 ± 2 vs. 34 ± 1 ms) and decay (time constant, 61 ± 3 vs. 49 ± 3 ms). Diabetic rats had a longer LV action potential (APD50, 98 ± 5 vs. 62 ± 5 ms; P &lt; 0.0001). Western blotting showed that diabetic rats had a reduced expression of sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA)2a, with no difference in expression of the Na+/Ca2+ exchanger. Immunohistochemistry of LV free wall showed that type I collagen was increased in diabetic rats (diabetic 7.1 ± 0.1%, control 12.7 ± 0.1%; P &lt; 0.01), and F-actin content reduced (diabetic 56.9 ± 0.6%; control 61.7 ± 0.4%; P &lt; 0.0001) with a disrupted structure.
CONCLUSIONS—We find no evidence to support the idea that altered Ca2+ homeostasis underlies the contractile deficit of diabetic cardiomyopathy. The slower action potential and reduced SERCA2a expression can explain the slower Ca2+ transient kinetics in diabetic rats but not the contractile deficit. Instead, we suggest that the observed LV remodeling may play a crucial role.
Blood Glucose Monitoring: A Practical Guide for Use in the Office and Clinic Setting
Authors: Odegard Peggy Soule , Beach Jennifer Rose 
Published: May 2008

In Brief
Interpretation of self-monitoring of blood glucose (SMBG) results is not routinely practiced in the office and clinic setting. However, such interpretation in the presence of patients may facilitate improved patient-provider discussion, clinical decisions, and ability to manage glycemic patterns. This review outlines key steps in a systematic review of SMBG data, including 1) identifying the degree of blood glucose control using mean and standard deviation or variance, 2) identifying patient safety concerns with regard to hypoglycemia, and 3)understanding the factors influencing blood glucose control by noting trends and patterns. Case studies are provided to illustrate the process for using and interpreting electronic SMBG downloads.
“It Feels Like Home When You Eat Rice and Beans”:Perspectives of Urban Latinos Living With Diabetes
Authors: Caban Arlene , Walker Elizabeth A. , Sanchez Severa , Mera Maria S. 
Published: May 2008

Background. Studies on Hispanics/Latinos with diabetes have largely focused on Mexican-American populations. This qualitative study explored psychosocial issues that affect diabetes self-management for Hispanic men and women of primarily Caribbean ancestry.Methods. Thirty-seven adults with diabetes in Bronx, N.Y., were recruited to seven focus groups, which were conducted in Spanish and English,audiotaped, transcribed, and subjected to qualitative analysis.Results. New themes emerged that are not well documented in the research literature for Hispanic/Latino populations with diabetes. These include the effect of diabetes on sexual health problems, perceptions about the link between depression and diabetes, intergenerational issues and their impact on participants' beliefs about diabetes, and perceptions of discrimination and discontinuity in health care.Conclusions. Findings suggest that perspectives among Hispanic/Latino populations about living with diabetes are diverse, and more research is needed. Social-cognitive theory and socio-ecological models of health may be useful to diabetes health care professionals in understanding patients' experiences with diabetes and informing the development of psychosocial and educational interventions that consider individuals and their environment.