bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Stochastic Edge in Adaptive Evolution
Authors: Brunet Éric , Rouzine Igor M , Wilke Claus O 
Published: May 2008

Abstract
In a recent article, Desai and Fisher proposed that the speed of adaptation in an asexual population is determined by the dynamics of the stochastic edge of the population, that is, by the emergence and subsequent establishment of rare mutants that exceed the fitness of all sequences currently present in the population. Desai and Fisher perform an elaborate stochastic calculation of the mean time τ until a new class of mutants has been established and interpret 1/τ as the speed of adaptation. As they note, however, their calculations are valid only for moderate speeds. This limitation arises from their method to determine τ: Desai and Fisher back extrapolate the value of τ from the best-fit class's exponential growth at infinite time. This approach is not valid when the population adapts rapidly, because in this case the best-fit class grows nonexponentially during the relevant time interval. Here, we substantially extend Desai and Fisher's analysis of the stochastic edge. We show that we can apply Desai and Fisher's method to high speeds by either exponentially back extrapolating from finite time or using a nonexponential back extrapolation. Our results are compatible with predictions made using a different analytical approach (Rouzine et al.) and agree well with numerical simulations.
Statistical Power Analysis of Neutrality Tests Under Demographic Expansions, Contractions and Bottlenecks With Recombination
Authors: Ramírez-Soriano Anna , Ramos-Onsins Sebastià E , Rozas Julio , Calafell Francesc , Navarro Arcadi 
Published: May 2008

Abstract
Several tests have been proposed to detect departures of nucleotide variability patterns from neutral expectations. However, very different kinds of evolutionary processes, such as selective events or demographic changes, can produce similar deviations from these tests, thus making interpretation difficult when a significant departure of neutrality is detected. Here we study the effects of demography and recombination upon neutrality tests by analyzing their power under sudden population expansions, sudden contractions, and bottlenecks. We evaluate tests based on the frequency spectrum of mutations and the distribution of haplotypes and explore the consequences of using incorrect estimates of the rates of recombination when testing for neutrality. We show that tests that rely on haplotype frequencies—especially Fs and ZnS, which are based, respectively, on the number of different haplotypes and on the r2 values between all pairs of polymorphic sites—are the most powerful for detecting expansions on nonrecombining genomic regions. Nevertheless, they are strongly affected by misestimations of recombination, so they should not be used when recombination levels are unknown. Instead, class I tests, particularly Tajima's D or R2, are recommended.
Genomic Analysis of Adaptive Differentiation inDrosophila melanogaster
Authors: Turner Thomas L , Levine Mia T , Eckert Melissa L , Begun David J 
Published: May 2008

AbstractDrosophila melanogaster shows clinal variation along latitudinal transects on multiple continents for several phenotypes, allozyme variants, sequence variants, and chromosome inversions. Previous investigation suggests that many such clines are due to spatially varying selection rather than demographic history, but the genomic extent of such selection is unknown. To map differentiation throughout the genome, we hybridized DNA from temperate and subtropical populations to Affymetrix tiling arrays. The dense genomic sampling of variants and low level of linkage disequilibrium in D. melanogaster enabled identification of many small, differentiated regions. Many regions are differentiated in parallel in the United States and Australia, strongly supporting the idea that they are influenced by spatially varying selection. Genomic differentiation is distributed nonrandomly with respect to gene function, even in regions differentiated on only one continent, providing further evidence for the role of selection. These data provide candidate genes for phenotypes known to vary clinally and implicate interesting new processes in genotype-by-environment interactions, including chorion proteins, proteins regulating meiotic recombination and segregation, gustatory and olfactory receptors, and proteins affecting synaptic function and behavior. This portrait of differentiation provides a genomic perspective on adaptation and the maintenance of variation through spatially varying selection.
Control of Antagonistic Components of the Hedgehog Signaling Pathway by microRNAs in Drosophila
Authors: Friggi-Grelin Florence , Lavenant-Staccini Laurence , Therond Pascal 
Published: May 2008

Abstract
Hedgehog (Hh) signaling is critical for many developmental processes and for the genesis of diverse cancers. Hh signaling comprises a series of negative regulatory steps, from Hh reception to gene transcription output. We previously showed that stability of antagonistic regulatory proteins, including the coreceptor Smoothened (Smo), the kinesin-like Costal-2 (Cos2), and the kinase Fused (Fu), is affected by Hh signaling activation. Here, we show that the level of these three proteins is also regulated by a microRNA cluster. Indeed, the overexpression of this cluster and resulting microRNA regulation of the 3′-UTRs of smo, cos2, and fu mRNA decreases the levels of the three proteins and activates the pathway. Further, the loss of the microRNA cluster or of Dicer function modifies the 3′-UTR regulation of smo and cos2 mRNA, confirming that the mRNAs encoding the different Hh components are physiological targets of microRNAs. Nevertheless, an absence of neither the microRNA cluster nor of Dicer activity creates an hh-like phenotype, possibly due to dose compensation between the different antagonistic targets. This study reveals that a single signaling pathway can be targeted at multiple levels by the same microRNAs.
Population Structure and Inbreeding From Pedigree Analysis of Purebred Dogs
Authors: Calboli Federico C F , Sampson Jeff , Fretwell Neale , Balding David J 
Published: May 2008

AbstractDogs are of increasing interest as models for human diseases, and many canine population-association studies are beginning to emerge. The choice of breeds for such studies should be informed by a knowledge of factors such as inbreeding, genetic diversity, and population structure, which are likely to depend on breed-specific selective breeding patterns. To address the lack of such studies we have exploited one of the world's most extensive resources for canine population-genetics studies: the United Kingdom (UK) Kennel Club registration database. We chose 10 representative breeds and analyzed their pedigrees since electronic records were established around 1970, corresponding to about eight generations before present. We find extremely inbred dogs in each breed except the greyhound and estimate an inbreeding effective population size between 40 and 80 for all but 2 breeds. For all but 3 breeds, &gt;90% of unique genetic variants are lost over six generations, indicating a dramatic effect of breeding patterns on genetic diversity. We introduce a novel index Ψ for measuring population structure directly from the pedigree and use it to identify subpopulations in several breeds. As well as informing the design of canine population genetics studies, our results have implications for breeding practices to enhance canine welfare.
Genome Analysis of the Unicellular Green Alga Chlamydomonas reinhardtii Indicates an Ancient Evolutionary Origin for Key Pattern Recognition and Cell-Signaling Protein Families
Authors: Wheeler Glen L , Miranda-Saavedra Diego , Barton Geoffrey J 
Published: May 2008

Abstract
The evolution of specific cell signaling and adhesion domains may have played an important role in the transition to a multicellular existence in the metazoans. Genomic analysis indicates that several signaling domains predominately found in animals are also present in the unicellular green alga, Chlamydomonas reinhardtii. A large group of proteins is present, containing scavenger receptor cysteine-rich (SRCR) and C-type lectin domains, which function in ligand binding and play key roles in the innate immune system of animals. Chlamydomonas also contains a large family of putative tyrosine kinases, suggesting an important role for phosphotyrosine signaling in the green algae. These important signaling domains may therefore be widespread among eukaryotes and most probably evolved in ancestral eukaryotes before the divergence of the Opisthokonts (the animal and fungal lineage).
Genome Analysis of Chlamydomonas reinhardtii Reveals The Existence of Multiple, Compartmentalized Iron–Sulfur Protein Assembly Machineries of Different Evolutionary Origins
Authors: Godman James , Balk Janneke 
Published: May 2008

Abstract
The unicellular green alga Chlamydomonas reinhardtii is used extensively as a model to study eukaryotic photosynthesis, flagellar functions, and more recently the production of hydrogen as biofuel. Two of these processes, photosynthesis and hydrogen production, are highly dependent on iron–sulfur (Fe–S) enzymes. To understand how Fe–S proteins are assembled in Chlamydomonas, we have analyzed its recently sequenced genome for orthologs of genes involved in Fe–S cluster assembly. We found a total of 32 open reading frames, most single copies, that are thought to constitute a mitochondrial assembly pathway, mitochondrial export machinery, a cytosolic assembly pathway, and components for Fe–S cluster assembly in the chloroplast. The chloroplast proteins are also expected to play a role in the assembly of the H-cluster in [FeFe]-hydrogenases, together with the recently identified HydEF and HydG proteins. Comparison with the higher plant model Arabidopsis indicated a strong degree of conservation of Fe–S cofactor assembly pathways in the green lineage, the pathways being derived from different origins during the evolution of the photosynthetic eukaryote. As a haploid, unicellular organism with available forward and reverse genetic tools, Chlamydomonas provides an excellent model system to study Fe–S cluster assembly and its regulation in photosynthetic eukaryotes.
Green Transcription Factors: A Chlamydomonas Overview
Authors: Riaño-Pachón Diego Mauricio , Corrêa Luiz Gustavo Guedes , Trejos-Espinosa Raúl , Mueller-Roeber Bernd 
Published: May 2008

AbstractTranscription factors (TFs) control gene expression by interacting with cis-elements in target gene promoters. Transcription regulators (TRs) assist in controlling gene expression through interaction with TFs, chromatin remodeling, or other mechanisms. Both types of proteins thus constitute master controllers of dynamic transcriptional networks. To uncover such control elements in the photosynthetic green alga Chlamydomonas reinhardtii, we performed a comprehensive analysis of its genome sequence. In total, we identified 234 genes encoding 147 TFs and 87 TRs of ∼40 families. The set of putative TFs and TRs, including their transcript and protein sequences, domain architectures, and supporting information about putative orthologs, is available at http://plntfdb.bio.uni-potsdam.de/v2.0/. Twelve of 34 plant-specific TF families were found in at least one algal species, indicating their early evolutionary origin. Twenty-two plant-specific TF families and one plant-specific TR family were not observed in algae, suggesting their specific association with developmental or physiological processes characteristic to multicellular plants. We also analyzed the occurrence of proteins that constitute the light-regulated transcriptional network in angiosperms and found putative algal orthologs for most of them. Our analysis provides a solid ground for future experimental studies aiming at deciphering the transcriptional regulatory networks in green algae.
Diversification of the Core RNA Interference Machinery in Chlamydomonas reinhardtii and the Role of DCL1 in Transposon Silencing
Authors: Casas-Mollano J Armando , Rohr Jennifer , Kim Eun-Jeong , Balassa Eniko , van Dijk Karin , Cerutti Heriberto 
Published: May 2008

Abstract
Small RNA-guided gene silencing is an evolutionarily conserved process that operates by a variety of molecular mechanisms. In multicellular eukaryotes, the core components of RNA-mediated silencing have significantly expanded and diversified, resulting in partly distinct pathways for the epigenetic control of gene expression and genomic parasites. In contrast, many unicellular organisms with small nuclear genomes seem to have lost entirely the RNA-silencing machinery or have retained only a basic set of components. We report here that Chlamydomonas reinhardtii, a unicellular eukaryote with a relatively large nuclear genome, has undergone extensive duplication of Dicer and Argonaute polypeptides after the divergence of the green algae and land plant lineages. Chlamydomonas encodes three Dicers and three Argonautes with DICER-LIKE1 (DCL1) and ARGONAUTE1 being more divergent than the other paralogs. Interestingly, DCL1 is uniquely involved in the post-transcriptional silencing of retrotransposons such as TOC1. Moreover, on the basis of the subcellular distribution of TOC1 small RNAs and target transcripts, this pathway most likely operates in the nucleus. However, Chlamydomonas also relies on a DCL1-independent, transcriptional silencing mechanism(s) for the maintenance of transposon repression. Our results suggest that multiple, partly redundant epigenetic processes are involved in preventing transposon mobilization in this green alga.
A New Purple Fluorescent Color Marker for Genetic Studies inSaccharomyces cerevisiaeandCandida albicans
Authors: Keppler-Ross Sabine , Noffz Christine , Dean Neta 
Published: May 2008

AbstractThe ability to visualize cellular events by linking them to color or fluorescence changes has been an invaluable tool for biology. We describe a novel plasmid-borne color marker whose expression in yeast leads to purple-colored cells that are also brightly fluorescent. This dominant marker provides a useful tool for rapidly screening plasmid maintenance using a visual or fluorescence assay in both Saccharomyces cerevisiae and Candida albicans.
Reconstructing the Mitochondrial Protein Import Machinery of Chlamydomonas reinhardtii
Authors: Figueroa-Martínez Francisco , Funes Soledad , Franzén Lars-Gunnar , González-Halphen Diego 
Published: May 2008

Abstract
In Chlamydomonas reinhardtii several nucleus-encoded proteins that participate in the mitochondrial oxidative phosphorylation are targeted to the organelle by unusually long mitochondrial targeting sequences. Here, we explored the components of the mitochondrial import machinery of the green alga. We mined the algal genome, searching for yeast and plant homologs, and reconstructed the mitochondrial import machinery. All the main translocation components were identified in Chlamydomonas as well as in Arabidopsis thaliana and in the recently sequenced moss Physcomitrella patens. Some of these components appear to be duplicated, as is the case of Tim22. In contrast, several yeast components that have relatively large hydrophilic regions exposed to the cytosol or to the intermembrane space seem to be absent in land plants and green algae. If present at all, these components of plants and algae may differ significantly from their yeast counterparts. We propose that long mitochondrial targeting sequences in some Chlamydomonas mitochondrial protein precursors are involved in preventing the aggregation of the hydrophobic proteins they carry.
Metabolomics- and Proteomics-Assisted Genome Annotation and Analysis of the Draft Metabolic Network of Chlamydomonas reinhardtii
Authors: May Patrick , Wienkoop Stefanie , Kempa Stefan , Usadel Björn , Christian Nils , Rupprecht Jens , Weiss Julia , Recuenco-Munoz Luis , Ebenhöh Oliver , Weckwerth Wolfram , Walther Dirk 
Published: May 2008

Abstract
We present an integrated analysis of the molecular repertoire of Chlamydomonas reinhardtii under reference conditions. Bioinformatics annotation methods combined with GCxGC/MS-based metabolomics and LC/MS-based shotgun proteomics profiling technologies have been applied to characterize abundant proteins and metabolites, resulting in the detection of 1069 proteins and 159 metabolites. Of the measured proteins, 204 currently do not have EST sequence support; thus a significant portion of the proteomics-detected proteins provide evidence for the validity of in silico gene models. Furthermore, the generated peptide data lend support to the validity of a number of proteins currently in the proposed model stage. By integrating genomic annotation information with experimentally identified metabolites and proteins, we constructed a draft metabolic network for Chlamydomonas. Computational metabolic modeling allowed an identification of missing enzymatic links. Some experimentally detected metabolites are not producible by the currently known and annotated enzyme set, thus suggesting entry points for further targeted gene discovery or biochemical pathway research. All data sets are made available as supplementary material as well as web-accessible databases and within the functional context via the Chlamydomonas-adapted MapMan annotation platform. Information of identified peptides is also available directly via the JGI-Chlamydomonas genomic resource database (http://genome.jgi-psf.org/Chlre3/Chlre3.home.html).
Awakening an Old Field—A Case Study of a Refracturing Program in the Greater Green River Basin
Authors: Shaefer Mark 
Published: May 2008

Summary
Restimulation of wells completed in the Frontier Formation, a low-permeability (e.g., 0.01–0.05 md) gas sand, has proved to be successful in the Fontenelle Field. The field is east of the Fon-tenelle reservoir, on the LaBarge Platform in the western part of the Greater Green River Basin in southwestern Wyoming. In this area the majority of hydrocarbon reserves in the Second Frontier are produced from the massive shoreface sandstones locally known as the Second Bench of the Second Frontier (Kf22b).
To date, Berco Resources, LLC has increased reserves in the Fontenelle Field by restimulating four wells producing from the Frontier Formation with massive hydraulic fracturing treatments. Because of the success of these treatments, another operator in an offset area to the north has also successfully implemented a Frontier refracturing program. This paper summarizes the refracturing program and the success which Berco Resources, LLC has realized. The candidate selection process is examined, as well as operational considerations when restimulating old wells. The stimulation treatments and fluid systems are also investigated. Daily/monthly production data consisting of gas, condensate, and water rates along with well head pressures are evaluated for all cases with fractured well type curves, the pseudoradial flow specialty plot (Δp/q vs. log t), and a production simulator comparing actual versus modeled production rates. Finally, the impact of the refrac-turing treatments on economic return is presented. The success of the refracture treatments has led to a new drilling/completion program in the Fontenelle Field in 2006 by an operator that recently acquired theBerco Resources, LLC properties.
Modeling Nonisothermal Rapid Multiphase Flow in Wells Under Nonequilibrium Conditions
Authors: Michel Guillermo , Civan Faruk 
Published: May 2008

Summary
An improved nonisothermal mathematical model considering the nonequilibrium effects involved during rapid multiphase flow in wells is presented. The extent of the nonequilibrium effect on deviation from the equilibrium-model predictions is delineated at various flow rates, fluid saturations, and temperatures. Applications for twophase (oil/gas) and three-phase (oil/water/gas) systems are presented. The model presented here can be coupled with reservoir simulation for accurate representation of the well-fluid hydraulics under non-equilibrium- and nonisothermal-flow conditions.
Fracture Acidizing: What Role Does Formation Softening Play in Production Response?
Authors: Nasr-El-Din H. A. , Al-Driweesh S. M. , Metcalf A. S. , Chesson J. B. 
Published: May 2008

Summary
Fracture acidizing of carbonates has yielded increases in production in many areas of the world, but depending on rock strength and reservoir closure pressure, this response may be lower than expected. Also, as a result of rock strength and closure pressure, production may decline at a higher rate than following a proppant fracture treatment.
Laboratory results are presented describing the effect of various acid systems on the strength reduction of limestone and dolomite-formation rock samples. Formation samples were dry or saturated with 2-wt% potassium chloride brine before testing. Samples were exposed to neat, emulsified, gelled, and crosslinked 15-wt% hydrochloric acids (HCl) and each exhibited a differing effect on rock-strength reduction. In addition, production responses are presented and compared with regard to the type of acid system used for stimulation.
On the basis of the results obtained, acid-system choices made a significant difference in the degree of rock softening of carbonates. Emulsified acid caused the least softening effect on limestone and dolomite cores. Softening effects were greater on limestone than on dolomite rocks. Production responses from emulsified-acid treatments were best.
Formation Damage Through Asphaltene Precipitation Resulting From CO2 Gas Injection in Iranian Carbonate Reservoirs
Authors: Kalantari Dahaghi Amirmasoud , Gholami Vida , Moghadasi Jamshid , Abdi R. 
Published: May 2008

Summary
Although carbon dioxide (CO2) injection is one of the most common enhanced-oil recovery methods that is widely used in many reservoirs, it may change the reservoir-fluid properties and cause problems such as asphaltene precipitation that will result in reduction of injectivity and productivity of oil wells and plugging of wellbores and production facilities.
This paper describes the effect of a miscible CO2 flood on asphaltene precipitation in the Bangestan reservoir of the Kupal field in southwest Iran. The amount of asphaltene precipitation in the mixture of oil and CO2 gas was measured by means of a PVT (pressure/volume/temperature) test, and the mechanism of precipitation under reservoir conditions was obtained by a high-pressure coreflood test. Then, the experimental results were compared with those obtained from available asphaltene-precipitation models.