bluuebunny/crossref_metadata_2025_split huggingface dataset:
A minor role of WNK3 in regulating phosphorylation of renal NKCC2 and NCC co-transporters in vivo
Authors: Oi Katsuyuki , Sohara Eisei , Rai Tatemitsu , Misawa Moko , Chiga Motoko , Alessi Dario R. , Sasaki Sei , Uchida Shinichi 
Published: December 2011

Summary
Mutations in WNK1 and WNK4 kinase genes have been shown to cause a human hereditary hypertensive disease, pseudohypoaldosteronism type II (PHAII). We previously discovered that WNK kinases phosphorylate and activate OSR1/SPAK kinases that regulate renal SLC12A family transporters such as NKCC2 and NCC, and clarified that the constitutive activation of this cascade causes PHAII. WNK3, another member of the WNK kinase family, was reported to be a strong activator of NCC/NKCC2 when assayed in Xenopus oocytes, suggesting that WNK3 also plays a major role in regulating blood pressure and sodium reabsorption in the kidney. However, it remains to be determined whether WNK3 is in fact involved in the regulation of these transporters in vivo. To clarify this issue, we generated and analyzed WNK3 knockout mice. Surprisingly, phosphorylation and expression of OSR1, SPAK, NKCC2 and NCC did not decrease in knockout mouse kidney under normal and low-salt diets. Similarly, expression of epithelial Na channel and Na/H exchanger 3 were not affected in knockout mice. Na+ and K+ excretion in urine in WNK3 knockout mice was not affected under different salt diets. Blood pressure in WNK3 knockout mice was not lower under normal diet. However, lower blood pressure was observed in WNK3 knockout mice fed low-salt diet. WNK4 and WNK1 expression was slightly elevated in the knockout mice under low-salt diet, suggesting compensation for WNK3 knockout by these WNKs. Thus, WNK3 may have some role in the WNK-OSR1/SPAK-NCC/NKCC2 signal cascade in the kidney, but its contribution to total WNK kinase activity may be minimal.
Experimental and Numerical Investigations of Ferrocene-Doped Propene Flames
Authors: Staude Susanne , Bergmann Ulf , Atakan Burak 
Published: December 2011

Abstract
Ferrocene-doped low-pressure, laminar, premixed propene/oxygen/argon flames of different stoichiometries were investigated experimentally using laser induced fluorescence (LIF) and the results were compared with numerical simulations. The influence of ferrocene on the flame temperature proved to be minimal both in the measurement and in the simulation. The measured flame temperatures were 100–250 K below the adiabatic flame temperature, as expected. However, the modeled flame temperatures were around 450 K below the measurements. It is assumed that the reason for this lies in the incorrect modeling of the flame speed since systematic errors in the LIF measurements should be small, as discussed in the paper. Iron atom concentrations were also measured using LIF. The results show the influence of the stoichiometry on the iron atom concentration, which is also reproduced by the model. The majority of the added iron was observed to exist as atomic iron in the flame. As more oxygen becomes available in leaner flames, iron will tend to form more FeO so that the iron atom concentration decreases with decreasing equivalence ratio.
The Effect of Carbon–Carbon Double Bonds on the Combustion Chemistry of Small Fatty Acid Esters
Authors: Yang Bin , Westbrook Charles K. , Cool Terrill A. , Hansen Nils , Kohse-Höinghaus Katharina 
Published: December 2011

Abstract
Environmentally friendly biodiesel is a mixture of saturated and unsaturated methyl (or ethyl) esters of long-chain fatty acids. To experimentally examine the effect of C=C double bonds on the combustion chemistry of fatty acid esters, low-pressure premixed laminar flames of four small esters have been studied using flame-sampling molecular-beam mass spectrometry. Mole fraction profiles of reactants, products, and well-identified stable and reactive combustion intermediates in flames of the saturated species methyl propanoate (CH3CH2COOCH
3) and its isomer ethyl acetate (CH3COOCH2CH
3) have been compared with results from flames of the unsaturated fuels methyl propenoate (CH2CHCOOCH
3) and vinyl acetate (CH3COOCHCH
2) flames. A total of eight flames have been studied, with two fuel-rich flame conditions investigated (fuel-equivalence ratios φ=1.2 and 1.56) for each fuel. In addition, the underlying oxidation chemistry at these premixed flame conditions has been investigated using a detailed chemical kinetic reaction mechanism, which is largely based on a previously proposed model for saturated esters [B. Yang et al., Phys. Chem. Chem. Phys. 13 (2011) 7205]. The combined results provide a detailed understanding of the similarities and differences between the combustion of saturated vs. unsaturated esters. Meanwhile, the isomeric and stoichiometric effects on their combustion chemistry are also addressed. In this paper, experimental and modeling details are discussed with a special focus on the different reaction pathways.
PLIF Thermometry Based on Measurements of Absolute Concentrations of the OH Radical
Authors: Heinze Johannes , Meier Ulrich , Behrendt Thomas , Willert Chris , Geigle Klaus-Peter , Lammel Oliver , Lückerath Rainer 
Published: December 2011

Abstract
A method for measurements of planar temperature distributions based on planar laser-induced fluorescence (PLIF) of the OH radiacal is described. The technique was developed specifically for the application in lean combustion systems, where OH equilibrium concentrations are largely independent on equivalence ratio and a function of temperature only. It is thus possible to derive a temperature information from measurements of absolute OH concentration, which can be obtained from a combined PLIF/absorption measurement.
This paper discusses the basics of the method, and describes validation experiments in high pressure laminar premixed flames which were performed to asses its applicability and accuracy. Therefore, we compared our LIF based results with CARS measurements performed in the same flames. Finally, an example for the application in a lean gas turbine model combustor is discussed.
Diode Laser Induced Fluorescence for Gas-Phase Diagnostics
Authors: Burns Iain S. , Kaminski Clemens F. 
Published: December 2011

Abstract
We highlight the capabilities and potential of diode laser induced fluorescence for measurements in gas-phase reacting flows. Many applications of diode lasers in practical sensing are based on absorption spectroscopy. Fluorescence-based diagnostics possess similar advantages in terms of practicality and implementation-cost but additionally are capable of achieving excellent spatial resolution. Diode laser fluorescence instruments have been employed for high-sensitivity trace gas monitoring in applications ranging from plasma physics to atmospheric chemistry. This article begins by describing the UV-visible diode laser technology used to perform fluorescence. The principles of diode laser induced fluorescence are then reviewed and a comparison is made with absorption spectroscopy. Examples are given of concentration measurements of both atomic and molecular trace gases. Recent work on using diode laser induced atomic fluorescence for precision measurements of flame temperature is also reviewed. We conclude by a discussion of future opportunities for diode laser fluorescence spectroscopy drawing attention to interesting potential target species as well as novel application areas, such as monitoring of synthesis processes for nanomaterials.
Response of Bacillus thuringiensis Al Hakam Endospores to Gas Dynamic Heating in a Shock Tube
Authors: McCartt A. Daniel , Gates Sean D. , Jeffries Jay B. , Hanson Ronald K. , Joubert Lydia M. , Buhr Tony L. 
Published: December 2011

Abstract
Experiments were conducted in a gas-driven shock tube to investigate shock wave-induced damage to Bacillus
thuringiensis Al Hakam endospores over a wide range of post-shock temperatures in non-oxidative gas environments. The results were compared with previous studies on B. atrophaeus and B. subtilis and demonstrate that B. thuringiensis Al Hakam exhibited a qualitatively similar response to rapid shock heating, even though this strain has a significantly different endospore structure. B.
thuringiensis Al Hakam endospores were nebulized into an aqueous aerosol, which was loaded into the Stanford aerosol shock tube, and subjected to shock waves of controlled strength. Endospores experienced uniform test temperatures between 500 and 1000 K and pressures ranging from 2 atm to 7 atm for approximately 2.5 ms. During this process the bio-aerosol was monitored using in situ time-resolved laser absorption and scattering diagnostics. Additionally, shock-treated bio-aerosol samples were extracted for ex situ analysis including viability plating, flow cytometry and scanning electron microscopy (SEM) imaging. B. thuringiensis Al Hakam endospores lost the ability to form colonies at post-shock temperatures above 500 K while significant breakdown in morphology was observed only for post-shock temperatures above 700 K. While viability loss and endospore morphological deterioration adhere to a similar framework across all endospore species studied, phenomena unique to B. thuringiensis Al Hakam were noted in the SEM images and optical extinction data. This initial characterization of the response of B. thuringiensis Al Hakam spores treated with shock/blast waves shows that these methods have potential for spore inactivation and detection.
Numerical Analysis of Thermoacoustic Instabilities Using LES and Computational Aeroacoustics
Authors: Klewer Christian , Ketelheun Anja , Janicka Johannes 
Published: December 2011

Abstract
Many technical combustion devices are susceptible to thermoacoustic instabilities. A deeper understanding of this transient phenomenon as well as the underlying physical processes is desirable. In this context, a turbulent enclosed flame is investigated numerically within this work by means of a hybrid LES/CAA (Large Eddy Simulation/Computational Aero Acoustics) approach as a step towards a numerical prediction of combustion instability. A thermoacoustically stable as well as a thermoacoustically unstable operating point are investigated. The LES computations reveal good overall agreement between simulation and experimental data. However, the recirculation zone, which is created by a backward facing step, is underestimated for the unstable case. The amplitudes as well as the frequencies of the simulated acoustic pressure are in good agreement with experimental data for the stable case. Considering the unstable case, the frequency of the oscillation is captured accurately, while the amplitudes are underpredicted.
On the Temperature Dependence of the Thermal Electron Attachment to SF
6
, SF
5
Cl, and POCl
3
Authors: Troe Hans-Jürgen , Marowsky Gerd , Shuman Nicholas S. , Miller Thomas M. , Viggiano Albert A. 
Published: December 2011

Abstract
A simplified model for electron attachment to neutral molecules, separating electron--phonon coupling (or intramolecular vibrational redistribution, IVR) factors into an electronic and a vibrational contribution, is tested by comparison with experimental results for the nondissociative electron attachments to SF6, SF5Cl, and POCl3. It is shown that the experimental results can approximately be reproduced by the fit of two parameters, one of them characterizing the dependence of the IVR factor on the electron energy and one accounting for an effective threshold energy for overlap of vibrational wave functions on anionic and neutral potential energy surfaces. After fitting these parameters, temperature dependences over wide ranges of conditions can be represented. Likewise, kinetic modeling of dissociative processes of the highly excited anions produced by attachment is facilitated.
A QTL Study for Regions Contributing toArabidopsis thalianaRoot Skewing on Tilted Surfaces
Authors: Vaughn Laura M , Masson Patrick H 
Published: December 2011

AbstractPlant root systems must grow in a manner that is dictated by endogenous genetic pathways, yet sensitive to environmental input. This allows them to provide the plant with water and nutrients while navigating a heterogeneous soil environment filled with obstacles, toxins, and pests. Gravity and touch, which constitute important cues for roots growing in soil, have been shown to modulate root architecture by altering growth patterns. This is illustrated by Arabidopsis thaliana roots growing on tilted hard agar surfaces. Under these conditions, the roots are exposed to both gravity and touch stimulation. Consequently, they tend to skew their growth away from the vertical and wave along the surface. This complex growth behavior is believed to help roots avoid obstacles in nature. Interestingly, A. thaliana accessions display distinct growth patterns under these conditions, suggesting the possibility of using this variation as a tool to identify the molecular mechanisms that modulate root behavior in response to their mechanical environment. We have used the Cvi/Ler recombinant inbred line population to identify quantitative trait loci that contribute to root skewing on tilted hard agar surfaces. A combination of fine mapping for one of these QTL and microarray analysis of expression differences between Cvi and Ler root tips identifies a region on chromosome 2 as contributing to root skewing on tilted surfaces, potentially by modulating cell wall composition.
Translational Genomics in Legumes Allowed Placing In Silico 5460 Unigenes on the Pea Functional Map and Identified Candidate Genes in Pisum sativum L.
Authors: Bordat Amandine , Savois Vincent , Nicolas Marie , Salse Jérome , Chauveau Aurélie , Bourgeois Michael , Potier Jean , Houtin Hervé , Rond Céline , Murat Florent , Marget Pascal , Aubert Grégoire , Burstin Judith 
Published: December 2011

Abstract
To identify genes involved in phenotypic traits, translational genomics from highly characterized model plants to poorly characterized crop plants provides a valuable source of markers to saturate a zone of interest as well as functionally characterized candidate genes. In this paper, an integrated view of the pea genetic map was developed. A series of gene markers were mapped and their best reciprocal homologs were identified on M. truncatula, L. japonicus, soybean, and poplar pseudomolecules. Based on the syntenic relationships uncovered between pea and M. truncatula, 5460 pea Unigenes were tentatively placed on the consensus map. A new bioinformatics tool, http://www.thelegumeportal.net/pea_mtr_translational_toolkit, was developed that allows, for any gene sequence, to search its putative position on the pea consensus map and hence to search for candidate genes among neighboring Unigenes. As an example, a promising candidate gene for the hypernodulation mutation nod3 in pea was proposed based on the map position of the likely homolog of Pub1, a M. truncatula gene involved in nodulation regulation. A broader view of pea genome evolution was obtained by revealing syntenic relationships between pea and sequenced genomes. Blocks of synteny were identified which gave new insights into the evolution of chromosome structure in Papillionoids and Eudicots. The power of the translational genomics approach was underlined.
Genetic Variation in the Chemical Components ofEucalyptus globulusWood
Authors: Stackpole Desmond J , Vaillancourt René E , Alves Ana , Rodrigues José , Potts Brad M 
Published: December 2011

AbstractDespite the ecological and economic importance of lignin and other wood chemical components, there are few studies of the natural genetic variation that exists within plant species and its adaptive significance. We used models developed from near infra-red spectroscopy to study natural genetic variation in lignin content and monomer composition (syringyl-to-guaiacyl ratio [S/G]) as well as cellulose and extractives content, using a 16-year-old field trial of an Australian tree species, Eucalyptus globulus. We sampled 2163 progenies of 467 native trees from throughout the native geographic range of the species. The narrow-sense heritability of wood chemical traits (0.25–0.44) was higher than that of growth (0.15), but less than wood density (0.51). All wood chemical traits exhibited significant broad-scale genetic differentiation (QST = 0.34–0.43) across the species range. This differentiation exceeded that detected with putatively neutral microsatellite markers (FST = 0.09), arguing that diversifying selection has shaped population differentiation in wood chemistry. There were significant genetic correlations among these wood chemical traits at the population and additive genetic levels. However, population differentiation in the S/G ratio of lignin in particular was positively correlated with latitude (R2 = 76%), which may be driven by either adaptation to climate or associated biotic factors.
Genome-Wide Analysis of Nascent Transcription in Saccharomyces cerevisiae
Authors: McKinlay Anastasia , Araya Carlos L , Fields Stanley 
Published: December 2011

Abstract
The assessment of transcriptional regulation requires a genome-wide survey of active RNA polymerases. Thus, we combined the nuclear run-on assay, which labels and captures nascent transcripts, with high-throughput DNA sequencing to examine transcriptional activity in exponentially growing Saccharomyces cerevisiae. Sequence read data from these nuclear run-on libraries revealed that transcriptional regulation in yeast occurs not only at the level of RNA polymerase recruitment to promoters but also at postrecruitment steps. Nascent synthesis signals are strongly enriched at TSS throughout the yeast genome, particularly at histone loci. Nascent transcripts reveal antisense transcription for more than 300 genes, with the read data providing support for the activity of distinct promoters driving transcription in opposite directions rather than bidirectional transcription from single promoters. By monitoring total RNA in parallel, we found that transcriptional activity accounts for 80% of the variance in transcript abundance. We computed RNA stabilities from nascent and steady-state transcripts for each gene and found that the most stable and unstable transcripts encode proteins whose functional roles are consistent with these stabilities. We also surveyed transcriptional activity after heat shock and found that most, but not all, heat shock-inducible genes increase their abundance by increasing their RNA synthesis. In summary, this study provides a genome-wide view of RNA polymerase activity in yeast, identifies regulatory steps in the synthesis of transcripts, and analyzes transcript stabilities.
Amino Acid Substitutions in the Caenorhabditis elegans RNA Polymerase II Large Subunit AMA-1/RPB-1 that Result in α-Amanitin Resistance and/or Reduced Function
Authors: Bowman Elizabeth Anne , Riddle Donald L , Kelly William 
Published: December 2011

Abstract
Mutations in the Caenorhabditis elegans RNA polymerase II AMA-1/RPB-1 subunit that cause α-amanitin resistance and/or developmental defects were isolated previously. We identified 12 of these mutations and mapped them onto the Saccharomyces cerevisiae RPB1 structure to provide insight into AMA-1 regions that are essential for development in a multicellular organism.
Genetic Background and Allorecognition Phenotype in Hydractinia symbiolongicarpus
Authors: Powell Anahid E , Moreno Maria , Gloria-Soria Andrea , Lakkis Fadi G , Dellaporta Stephen L , Buss Leo W 
Published: December 2011

Abstract
The Hydractinia allorecognition complex (ARC) was initially identified as a single chromosomal interval using inbred and congenic lines. The production of defined lines necessarily homogenizes genetic background and thus may be expected to obscure the effects of unlinked allorecognition loci should they exist. Here, we report the results of crosses in which inbred lines were out-crossed to wild-type animals in an attempt to identify dominant, codominant, or incompletely dominant modifiers of allorecognition. A claim for the existence of modifiers unlinked to ARC was rejected for three different genetic backgrounds. Estimates of the genetic map distance of ARC in two wild-type haplotypes differed markedly from one another and from that measured in congenic lines. These results suggest that additional allodeterminants exist in the Hydractinia ARC.
Modulation of the Activity of a Polycomb-Group Response Element in Drosophila by a Mutation in the Transcriptional Activator Woc
Authors: Noyes Amanda , Stefaniuk Catherine , Cheng Yuzhong , Kennison James A , Kassis Judith A 
Published: December 2011

Abstract
Polycomb group response elements (PRE) are cis-regulatory elements that bind Polycomb group proteins. We are studying a 181-bp PRE from the Drosophilaengrailed gene. This PRE causes pairing-sensitive silencing of mini-white in transgenes. Here we show that the 181-bp PRE also represses mini-white expression in flies with only one copy of the transgene. To isolate mutations that alter the activity of the 181-bp PRE, we screened for dominant suppressors of PRE-mediated mini-white repression. Dominant suppressors of mini-white repression were rare; we recovered only nine mutations out of 68,274 progeny screened. Two of the nine mutations isolated are due to the same single amino acid change in the transcriptional activator Woc (without children). Reversion experiments show that these are dominant gain-of-function mutations in woc. We suggest that Woc can interfere with the activity of the PRE. Our data have implications for how Polycomb group proteins act to either partially repress or completely silence their target genes.
A Genetic Screen for Dominant Enhancers of the Cell-Cycle Regulator α-Endosulfine Identifies Matrimony as a Strong Functional Interactor in Drosophila
Authors: Von Stetina Jessica R , LaFever Kimberly S , Rubin Mayer , Drummond-Barbosa Daniela 
Published: December 2011

Abstract
The coordination of cell-cycle events with developmental processes is essential for the reproductive success of organisms. In Drosophila melanogaster, meiosis is tightly coupled to oocyte development, and early embryos undergo specialized S-M mitoses that are supported by maternal products. We previously showed that the small phosphoprotein α-endosulfine (Endos) is required for normal oocyte meiotic maturation and early embryonic mitoses in Drosophila. In this study, we performed a genetic screen for dominant enhancers of endos00003 and identified several genomic regions that, when deleted, lead to impaired fertility of endos00003/+ heterozygous females. We uncovered matrimony (mtrm), which encodes a Polo kinase inhibitor, as a strong dominant enhancer of endos. mtrm126 +/+ endos00003 females are sterile because of defects in early embryonic mitoses, and this phenotype is reverted by removal of one copy of polo. These results provide compelling genetic evidence that excessive Polo activity underlies the strong functional interaction between endos00003 and mtrm126. Moreover, we show that endos is required for the increased expression of Mtrm in mature oocytes, which is presumably loaded into early embryos. These data are consistent with the model that maternal endos antagonizes Polo function in the early embryo to ensure normal mitoses through its effects on Mtrm expression during late oogenesis. Finally, we also identified genomic deletions that lead to loss of viability of endos00003/+ heterozygotes, consistent with recently published studies showing that endos is required zygotically to regulate the cell cycle during development.