bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic rate links density to demography in Tetrahymena pyriformis
Authors: DeLong John P , Hanson David T 
Published: July 2009

Abstract
Many populations show density-dependent growth rates. We suggest that population growth rate may be connected to density through the density dependence of metabolic rate. If metabolic rate is an index of the total biochemical work being done by an organism, then as populations grow and density suppresses metabolic rate, the rate of reproduction should slow and the ability to avoid death should diminish. To test this idea, we grew axenic populations of a single-celled protist, Tetrahymena pyriformis, in laboratory microcosms, and measured metabolic rate and density. We also estimated division (birth) and death rates. The proposed connection was supported by two observations. First, increasing population density suppressed per-capita metabolic rate in accordance with the predictions of a resource-division model. The same pattern was shown with experimentally altered densities. Second, per-capita metabolic rate was positively related to per-capita division rate and negatively related to per-capita death rate. Thus, the particular pattern of population growth and regulation depends on exactly how individuals respond energetically to the density of conspecifics, and how they allocate metabolism to maintenance and production. The physiological basis of population regulation in this system is based on the constraints imposed on the total metabolic work that individual cells can perform.
Signal transducer and activator of transcription 3 (STAT3) regulates adipocyte differentiation via peroxisome‐proliferator‐activated receptor γ (PPARγ)
Authors: Wang Dongmei , Zhou Yiran , Lei Weiwei , Zhang Kehua , Shi Jian , Hu Ying , Shu Guangwen , Song Jianguo 
Published: July 2009

Background information. STAT3 (signal transducer and activator of transcription 3) is an important transcription factor involved in many biological events, including apoptosis, tumorigenesis, angiogenesis and epithelial‐to‐mesenchymal transition. However, no direct evidence for a role of STAT3 in 3T3‐L1 adipocyte differentiation has been reported.Results. In the present study, we found that rapid activation of STAT3, lasting for more than 48 h, was elicited upon induction of adipogenesis. Both the STAT3‐selective inhibitor stattic and the JAK2 (Janus kinase 2)/STAT3‐selective inhibitors AG490 and Gö6976 inhibited STAT3 activation, leading to the suppression of adipocyte differentiation. Adipocyte differentiation was also suppressed by STAT3 siRNA (small interfering RNA) or dominant‐negative STAT3. Interestingly, the PPARγ (peroxisome‐proliferator‐activated receptor γ) agonist TAZ (troglitazone) abolished the STAT3‐inhibitor‐ and RNAi (RNA interference)‐mediated suppression of adipogenesis. However, TAZ treatment had no effect on the stattic‐ and AG490‐mediated down‐regulation of STAT3 activation, suggesting that STAT3 regulates adipocyte differentiation through signalling that occurs upstream of PPARγ.Conclusion. These data indicate that STAT3 functions as a critical factor for adipogenesis via a mechanism involving the PPARγ activation pathway.
Multiphase evaluation of myocardial bridging with dual-source computed tomography
Authors: Zhang Long Jiang , Yang Gui Fen , Zhou Chang Sheng , Huang Wei , Lu Guang Ming , Shiroishi M. S. 
Published: July 2009

Background: Myocardial bridging (MB), also known as a tunneled artery, is a congenital anomaly that can be readily diagnosed with multidetector-row computed tomography (MDCT). With the advent of dual-source CT (DSCT), it may be feasible to evaluate dynamic changes of MB throughout the entire cardiac cycle. Purpose: To determine the feasibility of dynamic evaluation of MB using DSCT. Material and Methods: Forty-eight patients with MB of the left anterior descending artery diagnosed with multiplanar reconstruction on DSCT were included in this study. Multiphase reconstructions were performed for every subject. Image quality was assessed using a four-point scale (4 = excellent; 3 = good; 2 = adequate; 1 = not assessable). Systolic and diastolic images with optimal image quality were selected. Milking effect, defined as the narrowing of the tunneled artery during systole and its dilatation during diastole, was recorded. The stenosis rate of MB was computed. Results: The optimal systolic and diastolic phases occurred between 40% and 70% of the R–R interval (range 20–80% of R–R interval). The image quality scores of all segments in systole and diastole were higher than or equal to 3. Diameter changes of tunneled vessel under MB in systole and diastole indicated milking effect, visualized on conventional coronary angiography (CAG). Average percentage of narrowing of the MB was 36±14%. Conclusion: High-quality systolic and diastolic images can be acquired using DSCT. Dynamic visualization of MB is possible, and milking effect can be quantified using DSCT.
Lower hybrid wave produced supra-thermal electrons and fishbone-like instability in FTU
Authors: Cesario R. , Panaccione L. , Botrugno A. , Calabrò G. , Cardinali A. , Castaldo C. , Marinucci M. , Pericoli V. , Romano A. , Smeulders P. , Tuccillo A.A. , Zonca F. 
Published: July 2009

The fishbone-like internal kink instability driven by supra-thermal electrons generated by lower hybrid current drive is an important issue of burning plasma research. Indeed, the trapped particle averaged bounce characterizing the interaction of trapped alpha particles with low-frequency MHD modes in burning plasmas depends on energy, not on mass, hence the charged fusion product effects can be usefully modelled by the analogous effect induced by the fast electrons on the low-frequency MHD modes.
Fishbone-like internal kink instabilities driven by electrons were observed during experiments on Frascati Tokamak Upgrade (FTU) and interpreted in terms of an oscillating ‘fixed point’ activity followed by one of ‘limit cycle’, produced by suprathermal electrons in the presence of a q-profile with q
min ≈ 1. As an interesting behaviour of the fast electron population produced by the LH power when the q-profile meets the condition q
min ≈ 1, the fast electron bremsstrahlung data of FTU show a marked redistribution in space across layers centred at r/a ≈ 0.20–0.33. This redistribution occurs during and in phase with the fishbone oscillation observed by the MHD diagnostic, with the same time scale and at the same radial position of the peak emission seen by x-ray tomography.
On the inference of spatial structure from population genetics data
Authors: Guillot Gilles 
Published: July 2009

Abstract
Motivation: In a series of recent papers, Tess, a computer program based on the concept of hidden Markov random field, has been proposed to infer the number and locations of panmictic population units from the genotypes and spatial locations of these individuals. The method seems to be of broad appeal as it is conceptually much simpler than other competing methods and it has been reported by its authors to be fast and accurate. However, this methodology is not grounded in a formal statistical inference method and seems to rely to a large extent on arbitrary choices regarding the parameters used. The present article is an investigation of the accuracy of this method and an attempt to assess whether recent results reported on the basis of this method are genuine features of the genetic process or artefacts of the method.
Method: I analyse simulated data consisting of populations at Hardy–Weinberg and linkage equilibrium and also data simulated under a scenario of isolation-by-distance at mutation–migration–drift equilibrium. Arabidopsis thaliana data previously analysed with this method are also reconsidered.
Results: Using the Tess program under the no-admixture model to analyse data consisting of several genuine HWLE populations with individuals of pure ancestries leads to highly inaccurate results; Using the Tess program under the admixture model to analyse data consisting of a continuous isolation-by-distance population leads to the inference of spurious HWLE populations whose number and features depend on the parameters used. Results previously reported about the A.thaliana using Tess seem to a large extent to be artefacts of the statistical methodology used. The findings go beyond population clustering models and can be an help to design more efficient algorithms based on graphs.
Availability: The data analysed in the present article are available from http://folk.uio.no/gillesg/Bioinformatics-HMRF
Contact: gilles.guillot@bio.uio.no
Supplementary information: Supplementary data are available at Bioinformatics online.
k-link EST clustering: evaluating error introduced by chimeric sequences under different degrees of linkage
Authors: Bragg Lauren M. , Stone Glenn 
Published: July 2009

Abstract
Motivation: The clustering of expressed sequence tags (ESTs) is a crucial step in many sequence analysis studies that require a high level of redundancy. Chimeric sequences, while uncommon, can make achieving the optimal EST clustering a challenge. Single-linkage algorithms are particularly vulnerable to the effects of chimeras. To avoid chimera-facilitated erroneous merges, researchers using single-linkage algorithms are forced to use stringent sequence–similarity thresholds. Such thresholds reduce the sensitivity of the clustering algorithm.
Results: We introduce the concept of k-link clustering for EST data. We evaluate how clustering error rates vary over a range of linkage thresholds. Using k-link, we show that Type II error decreases in response to increasing the number of shared ESTs (ie. links) required. We observe a base level of Type II error likely caused by the presence of unmasked low-complexity or repetitive sequence. We find that Type I error increases gradually with increased linkage. To minimize the Type I error introduced by increased linkage requirements, we propose an extension to k-link which modifies the required number of links with respect to the size of clusters being compared.
Availability: The implementation of k-link is available under the terms of the GPL from http://www.bioinformatics.csiro.au/products.shtml. k-link is licensed under the GNU General Public License, and can be downloaded from http://www.bioinformatics.csiro.au/products.shtml. k-link is written in C++.
Contact: lauren.bragg@csiro.au
Supplementary information: Supplementary data are available at Bioinformatics online.
Genome-wide maps of mono- and di-nucleosomes of Aspergillus fumigatus
Authors: Nishida Hiromi , Motoyama Takayuki , Yamamoto Shogo , Aburatani Hiroyuki , Osada Hiroyuki 
Published: July 2009

Abstract
We identified 5 975 567 mono- and 6 995 122 di-nucleosome positions of the fungus Aspergillus fumigatus, which was detected at high resolution based on the DNA sequence data obtained from both mono- and di-nucleosomal DNA fragments. We show that the distribution of lengths of the mono-nucleosomal DNA fragments has two peaks at 135 and 150 nt, whereas the distribution of di-nucleosomal DNA fragment lengths has a single peak at 285 nt. Although the gene bodies of the active and inactive genes and the inactive gene promoters had the two peaks of the mono-nucleosomal DNA fragment lengths, the active gene promoter lost the longer peak at 150 nt. Our findings strongly suggest that the nucleosomes protecting longer DNA fragments against MNase at the promoters, thereby inhibiting high gene expression.
Contact: hnishida@iu.a.u-tokyo.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Loss of Halophytism by Interference with SOS1 Expression
Authors: Oh Dong-Ha , Leidi Eduardo , Zhang Quan , Hwang Sung-Min , Li Youzhi , Quintero Francisco J. , Jiang Xingyu , D'Urzo Matilde Paino , Lee Sang Yeol , Zhao Yanxiu , Bahk Jeong Dong , Bressan Ray A. , Yun Dae-Jin , Pardo José M. , Bohnert Hans J. 
Published: July 2009

AbstractThe contribution of SOS1 (for Salt Overly Sensitive 1), encoding a sodium/proton antiporter, to plant salinity tolerance was analyzed in wild-type and RNA interference (RNAi) lines of the halophytic Arabidopsis (Arabidopsis thaliana)-relative Thellungiella salsuginea. Under all conditions, SOS1 mRNA abundance was higher in Thellungiella than in Arabidopsis. Ectopic expression of the Thellungiella homolog ThSOS1 suppressed the salt-sensitive phenotype of a Saccharomyces cerevisiae strain lacking sodium ion (Na+) efflux transporters and increased salt tolerance of wild-type Arabidopsis. thsos1-RNAi lines of Thellungiella were highly salt sensitive. A representative line, thsos1-4, showed faster Na+ accumulation, more severe water loss in shoots under salt stress, and slower removal of Na+ from the root after removal of stress compared with the wild type. thsos1-4 showed drastically higher sodium-specific fluorescence visualized by CoroNa-Green, a sodium-specific fluorophore, than the wild type, inhibition of endocytosis in root tip cells, and cell death in the adjacent elongation zone. After prolonged stress, Na+ accumulated inside the pericycle in thsos1-4, while sodium was confined in vacuoles of epidermis and cortex cells in the wild type. RNAi-based interference of SOS1 caused cell death in the root elongation zone, accompanied by fragmentation of vacuoles, inhibition of endocytosis, and apoplastic sodium influx into the stele and hence the shoot. Reduction in SOS1 expression changed Thellungiella that normally can grow in seawater-strength sodium chloride solutions into a plant as sensitive to Na+ as Arabidopsis.
Abscisic Acid Has a Key Role in Modulating Diverse Plant-Pathogen Interactions
Authors: Fan Jun , Hill Lionel , Crooks Casey , Doerner Peter , Lamb Chris 
Published: July 2009

AbstractWe isolated an activation-tagged Arabidopsis (Arabidopsis thaliana) line, constitutive disease susceptibility2-1D (cds2-1D), that showed enhanced bacterial growth when challenged with various Pseudomonas syringae strains. Systemic acquired resistance and systemic PATHOGENESIS-RELATED GENE1 induction were also compromised in cds2-1D. The T-DNA insertion adjacent to NINE-CIS-EPOXYCAROTENOID DIOXYGENASE5 (NCED5), one of six genes encoding the abscisic acid (ABA) biosynthetic enzyme NCED, caused a massive increase in transcript level and enhanced ABA levels &gt;2-fold. Overexpression of NCED genes recreated the enhanced disease susceptibility phenotype. NCED2, NCED3, and NCED5 were induced, and ABA accumulated strongly following compatible P. syringae infection. The ABA biosynthetic mutant aba3-1 showed reduced susceptibility to virulent P. syringae, and ABA, whether through exogenous application or endogenous accumulation in response to mild water stress, resulted in increased bacterial growth following challenge with virulent P. syringae, indicating that ABA suppresses resistance to P. syringae. Likewise ABA accumulation also compromised resistance to the biotrophic oomycete Hyaloperonospora arabidopsis, whereas resistance to the fungus Alternaria brassicicola was enhanced in cds2-1D plants and compromised in aba3-1 plants, indicating that ABA promotes resistance to this necrotroph. Comparison of the accumulation of salicylic acid and jasmonic acid in the wild type, cds2-1D, and aba3-1 plants challenged with P. syringae showed that ABA promotes jasmonic acid accumulation and exhibits a complex antagonistic relationship with salicylic acid. Our findings provide genetic evidence that the abiotic stress signal ABA also has profound roles in modulating diverse plant-pathogen interactions mediated at least in part by cross talk with the jasmonic acid and salicylic acid biotic stress signal pathways.
Arabidopsis Methionineγ-Lyase Is Regulated According to Isoleucine Biosynthesis Needs But Plays a Subordinate Role to Threonine Deaminase
Authors: Joshi Vijay , Jander Georg 
Published: July 2009

AbstractThe canonical pathway for isoleucine biosynthesis in plants begins with the conversion of threonine to 2-ketobutyrate by threonine deaminase (OMR1). However, demonstration of methionine γ-lyase (MGL) activity in Arabidopsis (Arabidopsis thaliana) suggested that production of 2-ketobutyrate from methionine can also lead to isoleucine biosynthesis. Rescue of the isoleucine deficit in a threonine deaminase mutant by MGL overexpression, as well as decreased transcription of endogenous Arabidopsis MGL in a feedback-insensitive threonine deaminase mutant background, shows that these two enzymes have overlapping functions in amino acid biosynthesis. In mgl mutant flowers and seeds, methionine levels are significantly increased and incorporation of [13C]Met into isoleucine is decreased, but isoleucine levels are unaffected. Accumulation of free isoleucine and other branched-chain amino acids is greatly elevated in response to drought stress in Arabidopsis. Gene expression analyses, amino acid phenotypes, and labeled precursor feeding experiments demonstrate that MGL activity is up-regulated by osmotic stress but likely plays a less prominent role in isoleucine biosynthesis than threonine deaminase. The observation that MGL makes a significant contribution to methionine degradation, particularly in reproductive tissue, suggests practical applications for silencing the expression of MGL in crop plants and thereby increasing the abundance of methionine, a limiting essential amino acid.
Comparative Large-Scale Analysis of Interactions between Several Crop Species and the Effector Repertoires from Multiple Pathovars of Pseudomonas and Ralstonia
Authors: Wroblewski Tadeusz , Caldwell Katherine S. , Piskurewicz Urszula , Cavanaugh Keri A. , Xu Huaqin , Kozik Alexander , Ochoa Oswaldo , McHale Leah K. , Lahre Kirsten , Jelenska Joanna , Castillo Jose A. , Blumenthal Daniel , Vinatzer Boris A. , Greenberg Jean T. , Michelmore Richard W. 
Published: July 2009

Abstract
Bacterial plant pathogens manipulate their hosts by injection of numerous effector proteins into host cells via type III secretion systems. Recognition of these effectors by the host plant leads to the induction of a defense reaction that often culminates in a hypersensitive response manifested as cell death. Genes encoding effector proteins can be exchanged between different strains of bacteria via horizontal transfer, and often individual strains are capable of infecting multiple hosts. Host plant species express diverse repertoires of resistance proteins that mediate direct or indirect recognition of bacterial effectors. As a result, plants and their bacterial pathogens should be considered as two extensive coevolving groups rather than as individual host species coevolving with single pathovars. To dissect the complexity of this coevolution, we cloned 171 effector-encoding genes from several pathovars of Pseudomonas and Ralstonia. We used Agrobacterium tumefaciens-mediated transient assays to test the ability of each effector to induce a necrotic phenotype on 59 plant genotypes belonging to four plant families, including numerous diverse accessions of lettuce (Lactuca sativa) and tomato (Solanum lycopersicum). Known defense-inducing effectors (avirulence factors) and their homologs commonly induced extensive necrosis in many different plant species. Nonhost species reacted to multiple effector proteins from an individual pathovar more frequently and more intensely than host species. Both homologous and sequence-unrelated effectors could elicit necrosis in a similar spectrum of plants, suggesting common effector targets or targeting of the same pathways in the plant cell.
Defining Core Metabolic and Transcriptomic Responses to Oxygen Availability in Rice Embryos and Young Seedlings
Authors: Narsai Reena , Howell Katharine A. , Carroll Adam , Ivanova Aneta , Millar A. Harvey , Whelan James 
Published: July 2009

AbstractAnalysis reveals that there is limited overlap in the sets of transcripts that show significant changes in abundance during anaerobiosis in different plant species. This may be due to the fact that a combination of primary effects, changes due to the presence or absence of oxygen, and secondary effects, responses to primary changes or tissue and developmental responses, are measured together and not differentiated from each other. In order to dissect out these responses, the effect of the presence or absence of oxygen was investigated using three different experimental designs using rice (Oryza sativa) as a model system. A total of 110 metabolites and 9,596 transcripts were found to change significantly in response to oxygen availability in at least one experiment. However, only one-quarter of these showed complementary responses to oxygen in all three experiments, allowing the core response to oxygen availability to be defined. A total of 10 metabolites and 1,136 genes could be defined as aerobic responders (up-regulated in the presence of oxygen and down-regulated in its absence), and 13 metabolites and 730 genes could be defined as anaerobic responders (up-regulated in the absence of oxygen and down-regulated in its presence). Defining core sets of transcripts that were sensitive to oxygen provided insights into alterations in metabolism, specifically carbohydrate and lipid metabolism and the putative regulatory mechanisms that allow rice to grow under anaerobic conditions. Transcript abundance of a specific set of transcription factors was sensitive to oxygen availability during all of the different experiments conducted, putatively identifying primary regulators of gene expression under anaerobic conditions. Combined with the possibility of selective transcript degradation, these transcriptional processes are involved in the core response of rice to anaerobiosis.
BOBBER1Is a Noncanonical Arabidopsis Small Heat Shock Protein Required for Both Development and Thermotolerance
Authors: Perez Dahlia E. , Hoyer J. Steen , Johnson Ayanna I. , Moody Zachary R. , Lopez Joseph , Kaplinsky Nicholas J. 
Published: July 2009

AbstractPlants have evolved a range of cellular responses to maintain developmental homeostasis and to survive over a range of temperatures. Here, we describe the in vivo and in vitro functions of BOBBER1 (BOB1), a NudC domain containing Arabidopsis (Arabidopsisthaliana) small heat shock protein. BOB1 is an essential gene required for the normal partitioning and patterning of the apical domain of the Arabidopsis embryo. Because BOB1 loss-of-function mutants are embryo lethal, we used a partial loss-of-function allele (bob1-3) to demonstrate that BOB1 is required for organismal thermotolerance and postembryonic development. Recombinant BOB1 protein functions as a molecular chaperone and prevents the aggregation of a model protein substrate in vitro. In plants, BOB1 is cytoplasmic at basal temperatures, but forms heat shock granules containing canonical small heat shock proteins at high temperatures. In addition to thermotolerance defects, bob1-3 exhibits pleiotropic development defects during all phases of development. bob1-3 phenotypes include decreased rates of shoot and root growth as well as patterning defects in leaves, flowers, and inflorescence meristems. Most eukaryotic chaperones play important roles in protein folding either during protein synthesis or during cellular responses to denaturing stress. Our results provide, to our knowledge, the first evidence of a plant small heat shock protein that has both developmental and thermotolerance functions and may play a role in both of these folding networks.