bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental studies on the direct flexoelectric effect in α-phase polyvinylidene fluoride films
Authors: Baskaran Sivapalan , He Xiangtong , Chen Qin , Fu John Y.
Published: June 2011

We report observation of the giant direct flexoelectric effect in α-phase polyvinylidene fluoride (PVDF) films. This unexpected phenomenon was detected in the α-phase PVDF film undergoing elastic tensile stretching. Our results have shown that the physical mechanism behind the flexoelectricity in polymers might be more complicated than the one proposed for solid crystalline dielectrics.
Study on the electronic structure and the optical performance of YB6 by the first-principles calculations
Authors: Xiao Lihua , Su Yuchang , Chen Hongyang , Jiang Min , Liu Sainan , Hu Zexing , Liu Ruifeng , Peng Ping , Mu Yuanlong , Zhu Diya
Published: June 2011

The electronic structure and the optical performance of YB6 were investigated by first-principles calculations within the framework of density functional theory. It was found that the calculated results are in agreement with the relevant experimental data. Our theoretical studies showed that YB6 is a promising solar radiation shielding material for windows.
Unusual strategies for using indium gallium nitride grown on silicon (111) for solid-state lighting
Authors: Kim Hoon-sik , Brueckner Eric , Song Jizhou , Li Yuhang , Kim Seok , Lu Chaofeng , Sulkin Joshua , Choquette Kent , Huang Yonggang , Nuzzo Ralph G. , Rogers John A.
Published: June 2011

Properties that can now be achieved with advanced, blue indium gallium nitride light emitting diodes (LEDs) lead to their potential as replacements for existing infrastructure in general illumination, with important implications for efficient use of energy. Further advances in this technology will benefit from reexamination of the modes for incorporating this materials technology into lighting modules that manage light conversion, extraction, and distribution, in ways that minimize adverse thermal effects associated with operation, with packages that exploit the unique aspects of these light sources. We present here ideas in anisotropic etching, microscale device assembly/integration, and module configuration that address these challenges in unconventional ways. Various device demonstrations provide examples of the capabilities, including thin, flexible lighting “tapes” based on patterned phosphors and large collections of small light emitters on plastic substrates. Quantitative modeling and experimental evaluation of heat flow in such structures illustrates one particular, important aspect of their operation: small, distributed LEDs can be passively cooled simply by direct thermal transport through thin-film metallization used for electrical interconnect, providing an enhanced and scalable means to integrate these devices in modules for white light generation.
Sme4 coiled-coil protein mediates synaptonemal complex assembly, recombinosome relocalization, and spindle pole body morphogenesis
Authors: Espagne Eric , Vasnier Christelle , Storlazzi Aurora , Kleckner Nancy E. , Silar Philippe , Zickler Denise , Malagnac Fabienne
Published: June 2011

We identify a large coiled-coil protein, Sme4/PaMe4, that is highly conserved among the large group of Sordariales and plays central roles in two temporally and functionally distinct aspects of the fungal sexual cycle: first as a component of the meiotic synaptonemal complex (SC) and then, after disappearing and reappearing, as a component of the spindle pole body (SPB). In both cases, the protein mediates spatial juxtaposition of two major structures: linkage of homolog axes through the SC and a change in the SPB from a planar to a bent conformation. Corresponding mutants exhibit defects, respectively, in SC and SPB morphogenesis, with downstream consequences for recombination and astral-microtubule nucleation plus postmeiotic nuclear migration. Sme4 is also required for reorganization of recombination complexes in which Rad51, Mer3, and Msh4 foci relocalize from an on-axis position to a between-axis (on-SC) position concomitant with SC installation. Because involved recombinosome foci represent total recombinational interactions, these dynamics are irrespective of their designation for maturation into cross-overs or noncross-overs. The defined dual roles for Sme4 in two different structures that function at distinct phases of the sexual cycle also provide more functional links and evolutionary dynamics among the nuclear envelope, SPB, and SC.
Evaluation of Woundfin Augmentation Efforts in the Virgin River by Estimation of Admixture Proportions
Authors: Chen Yongjiu , Childs Michael R. , Keeler‐Foster Connie
Published: June 2011

The woundfin Plagopterus argentissimus is imperiled as a result of habitat destruction, water diversion, and the introduction of nonnative species. Augmentation of wild woundfin populations in the Utah portion of the Virgin River with fish from Dexter National Fish Hatchery and Technology Center (Dexter Hatchery) began in 2003. We used 10 microsatellite DNA loci to determine whether captive woundfins are contributing to recruitment in the Virgin River. Admixture analyses based on moment estimators, maximum likelihood, frequency, and Bayesian approaches indicated that the genetic contribution of Dexter Hatchery's woundfin augmentation stocking to 2005 recruitment in the Virgin River was 35–46% in the Washington Fields Diversion reach and 43–59% in the area of the Quail Creek Reservoir inflow. Salvaged wild parental stock was mixed with the captive broodstock at Dexter Hatchery in 2004 and had a genetic contribution of 26–49% to the offspring reared at Dexter Hatchery in 2005. Care must be taken to ensure the genetic integrity of stocked fish as the potential impact on the augmented population can be substantial. These results demonstrate that genetic markers used to infer gene flow (via admixture analysis) from the captive population to the wild population can be applied to determine the effectiveness of hatchery propagation programs and to monitor genetic similarity between wild and stocked fish.
Length and Age Trends of Chinook Salmon in the Nushagak River, Alaska, Related to Commercial and Recreational Fishery Selection and Exploitation
Authors: Kendall Neala W. , Quinn Thomas P.
Published: June 2011

Long‐term trends in fish age and size at maturation provide important insights into population stability as they are affected by changes in growing conditions. Fishery exploitation and selection can also induce such trends. It is important to identify the causes of changing life history patterns because they affect population dynamics and productivity. Average body sizes or ages of many western North American populations of Chinook salmon Oncorhynchus tshawytscha, including the Nushagak River population in Bristol Bay, Alaska, have declined over the past several decades. This population is caught in commercial, recreational, and subsistence fisheries and therefore represents an opportunity to compare fishery exploitation and selection and to examine their possible effects. We compiled data and examined trends in size and age at maturation between 1981 and 2009, and we then quantified commercial and recreational fishery exploitation and selection rates. The average age and lengths at most ages of maturing fish decreased over time. The commercial fishery caught the majority (73%) of the harvested fish annually compared with the recreational (9%) and subsistence fisheries (18%). Size selection by the commercial fishery was highly variable over time, but overall, smaller‐than‐average fish were caught, inconsistent with the declining trends in age and size of returning fish. In contrast, the recreational fishery and presumably the subsistence fishery regularly removed larger‐than‐average fish, consistent with the trends. However, the opposing selection by the commercial fishery suggests that the trends in age and size at maturation are unlikely to have been caused solely by fishery selection. Rather, the trends are probably also related to environmental changes affecting fish growth. Still, regulations that decrease either the allowable size of harvested Chinook salmon or the allowable number of large fish may help to decrease the size selectivity of the Nushagak River recreational and subsistence fisheries.
Partial Migration in a Robust Brown Trout Population of a Patagonian River
Authors: O'Neal Sarah L. , Stanford Jack A.
Published: June 2011

Life history plasticity, particularly partial migration (i.e., coexistence of resident and anadromous forms), probably plays a major role in the ability of brown troutSalmo truttato dominate food webs after introduction into Patagonian rivers. We documented brown trout establishment, distribution, and life history variation in relation to habitat features in the Rio Grande, Tierra del Fuego, Argentina. Results support the hypothesis that Rio Grande brown trout developed an anadromous life history form (“sea trout”) two decades after introduction in relation to localized food limitation as the population expanded throughout the basin. Tributary streams with only resident fish were narrower and had significantly higher levels of specific conductance and soluble reactive phosphorus than streams that were inhabited by both resident and anadromous brown trout. Invertebrate biomass was two to three times higher and juvenile brown trout density was significantly higher in resident‐only sites than in streams with both life history forms. Density‐dependent growth was not evident and juvenile condition was higher in resident‐only streams. These findings suggest that food availability influences the individual decision to migrate, although genetic and other factors are probably also involved. Mark–recapture analysis showed that approximately 38,000–55,000 adult sea trout returned annually to the Rio Grande in 2006 and 2007, making it one of the most robust sea trout populations in the world. However, native fishes have apparently declined to near extirpation as the brown trout population has expanded.
Home Range Size and Foraging Ecology of Bull Trout and Westslope Cutthroat Trout in the Upper Salmon River Basin, Idaho
Authors: Schoby Gregory P. , Keeley Ernest R.
Published: June 2011

We used radiotelemetry to determine how body size, foraging ecology, and seasonal activity influence the home range size of adult bull troutSalvelinus confluentusand westslope cutthroat troutOncorhynchus clarkii lewisiin the upper Salmon River basin of central Idaho. Stomach samples were collected to determine diet composition and compare foraging strategies between the two species. Contrary to other studies of home ranges for stream‐dwelling fishes, home range size was not significantly related to total length or body mass in either species. Although overall home range size did not differ between species, monthly movement (km) was significantly greater for bull trout than for westslope cutthroat trout during July and September. Stomach content analysis revealed that the size of prey consumed was significantly larger for bull trout than for westslope cutthroat trout but was not significantly correlated with body size in either species. Home range size for bull trout and westslope cutthroat trout in our study was much larger than home ranges documented for other stream‐dwelling salmonids; our results illustrate the importance of large‐scale connectivity and the variety of habitats necessary for the persistence of these species.
Land Use Associations with Distributions of Declining Native Fishes in the Upper Colorado River Basin
Authors: Dauwalter Daniel C. , Wenger Seth J. , Gelwicks Kevin R. , Fesenmyer Kurt A.
Published: June 2011

The upper Colorado River basin contains one of the most imperiled fish faunas in North America. Anthropogenic land use and nonnative species impacts are considered among the top reasons for imperilment. We determined the association of anthropogenic land use intensity (road density, percentage of converted land, and oil and gas well density), relative abundance of nonnative white suckersCatostomus commersoniiand their hybrids, and natural landscape features with the occurrences of three native fishes in the Colorado River basin, Wyoming, that have declined throughout their ranges: flannelmouth suckerC. latipinnis, bluehead suckerC. discobolus, and roundtail chubGila robusta. We found that flannelmouth suckers occurred more frequently in large, low‐gradient stream reaches, but their occurrence was not associated with land use intensity or the relative abundance of white suckers and hybrid suckers. In contrast, bluehead sucker occurrence decreased with increasing intensity of each land use type within a 0.5‐km stream buffer, which suggests that localized land use disturbances have negatively affected the species’ distribution. Roundtail chub occurred more frequently in low‐gradient stream segments with more riparian vegetation, but associations with land uses were more complex. Roundtail chub were negatively associated with road density in a 0.5‐km buffer, but in contrast to our expectations they were positively associated with road density in the contributing watershed and with local oil and gas well density. We think that rocky substrates and pools—habitats preferred by roundtail chub and sometimes associated with oil and gas infrastructure—have concentrated the remaining individuals within their currently reduced distribution. The associations we identified highlight the potential role of land use in distributional declines and can help managers to determine whether proposed land use changes may affect existing populations. Spatial predictions of occurrence have already been used in regional fish conservation planning efforts in Wyoming.
INTERSECTIONS, DIVISIONS, AND DISTINCTIONS
Authors: Taylor Yvette , Scurry Tracy
Published: June 2011

While there is a growing body of research which explores the dramatic changes of higher education, following recent policies of widening participation and ‘internationalisation’, to date much of the research has focused on discrete ‘non-traditional’ groups. Based on qualitative data gathered from international and widening participation students, we explore the crossovers and parallels of their experiences, which is not to say that both groups are the very same. Indeed, it is the resistance to a ‘fixing’ positioning that this paper charts, negotiating points of sameness and difference. We suggest that there is failure to consider widening participation and internationalisation as two, intersecting, agendas, (re)producing class and race. Theoretically, such an approach offers an insight into contemporary class analysis in the context of mobility and racism, to comprehend how social divisions are complexly lived, where middle-class ‘international’ students may risk losing (and gaining) privilege, in (dis)similar ways to their working-class ‘home’ counterparts.
Modeling Environments: Interactive Causation and Adaptations to Environmental Conditions
Authors: Glymour Bruce
Published: June 2011

I argue that a phenotypic trait can be an adaptation to a particular environmental condition, as against others, only if the environmental condition and the phenotype interactively cause fitness. Models of interactive environmental causes of fitness generally require that environments be individuated by explicit representation rather than by measures of environmental quality, although the latter understanding of ‘environment’ is more prominent in the philosophy of biology. Hence, talk of adaptations to some but not other environmental conditions relies on conceptions of ‘environment’ importantly different from that commonly presupposed in philosophy of biology.
Extension of a data-driven gating technique to 3D, whole body PET studies
Authors: Schleyer Paul J , O'Doherty Michael J , Marsden Paul K
Published: June 2011

Respiratory gating can be used to separate a PET acquisition into a series of near motion-free bins. This is typically done using additional gating hardware; however, software-based methods can derive the respiratory signal from the acquired data itself. The aim of this work was to extend a data-driven respiratory gating method to acquire gated, 3D, whole body PET images of clinical patients. The existing method, previously demonstrated with 2D, single bed-position data, uses a spectral analysis to find regions in raw PET data which are subject to respiratory motion. The change in counts over time within these regions is then used to estimate the respiratory signal of the patient. In this work, the gating method was adapted to only accept lines of response from a reduced set of axial angles, and the respiratory frequency derived from the lung bed position was used to help identify the respiratory frequency in all other bed positions. As the respiratory signal does not identify the direction of motion, a registration-based technique was developed to align the direction for all bed positions. Data from 11 clinical FDG PET patients were acquired, and an optical respiratory monitor was used to provide a hardware-based signal for comparison. All data were gated using both the data-driven and hardware methods, and reconstructed. The centre of mass of manually defined regions on gated images was calculated, and the overall displacement was defined as the change in the centre of mass between the first and last gates. The mean displacement was 10.3 mm for the data-driven gated images and 9.1 mm for the hardware gated images. No significant difference was found between the two gating methods when comparing the displacement values. The adapted data-driven gating method was demonstrated to successfully produce respiratory gated, 3D, whole body, clinical PET acquisitions.
Synthesis, characterization and luminescent properties of Tb(III) doped Eu(III) complex nanoparticles
Authors: Hoang Thi Khuyen , Nguyen Thanh Huong , Tran Thu Huong , Tran Kim Anh , Nguyen Thanh Binh , Le Quoc Minh
Published: June 2011

In recent years, considerable effort has been devoted to the development of transition metal complexes as novel luminescent materials that have potential application in the fluorescent labels for chemistry or biology. Among them, the nanostructured lanthanide complexes have been receiving much attention because of their excellent luminescence properties, which are attributed to the intramolecular energy transfer between the ligands and chelated lanthanide ions and their high solubility in water. This paper presents some results of the synthesis and characterization of the nanoparticles of Eu(III) and Tb(III) complexes with naphthoyl trifluoroacetone and tri-n-octylphosphineoxide. In addition, the influence of the dopant Tb(III) on the photophysical properties of the system of lanthanide complexes of Eu(III) and Tb(III) is also studied.
Influence of climate-driven sea surface temperature increase on potential habitats of the Pacific saury (Cololabis saira)
Authors: Tseng Chen-Te , Sun Chi-Lu , Yeh Su-Zan , Chen Shih-Chin , Su Wei-Cheng , Liu Don-Chung
Published: June 2011

Tseng, C-T., Sun, C-L., Yeh, S-Z., Chen, S-C., Su, W-C., and Liu, D-C. 2011. Influence of climate-driven sea surface temperature increase on potential habitats of the Pacific saury (Cololabis saira). – ICES Journal of Marine Science, 68: 1105–1113. Logbook data of the 2006–2008 Taiwanese Pacific saury fishery, coupled with MODIS satellite-derived sea surface temperature (SST) data, were used to determine Pacific saury's SST preferences and predict their potential habitats monthly. Results indicated that the SST preferences ranged from 12 to18.5°C, with significant monthly variability. Possible changes in potential saury habitats were estimated under four scenarios: recent years (2006–2008) and with 1, 2, and 4°C increases in SST because of climate change. Results revealed an obvious poleward shift of potential saury habitats under the influence of increases in SSTs. The southernmost boundary of potential saury habitat in recent years, located at 40.24°N, shifted to 46.15°N under the scenario of a 4°C increase in SSTs. These results improve our understanding of the variability in the spatial distribution of saury habitats and could form the basis for future fishery management and fishing forecasts.
Environmental controls of phenology of high-latitude Chinook salmon populations of the Yukon River, North America, with application to fishery management
Authors: Mundy Phillip R. , Evenson Danielle F.
Published: June 2011

Mundy, P. R., and Evenson, D. F. 2011. Environmental controls of phenology of high-latitude Chinook salmon populations of the Yukon River, North America, with application to fishery management. – ICES Journal of Marine Science, 68: 1155–1164. Phenologies of a number of anadromous fish species have been demonstrated to vary in concert with environmental factors that change with global warming, such as water and air temperatures. Anadromous fishery managers will need advice from models of phenology, or migratory timing, as functions of environmental factors in those harvest areas where annual migratory timing can vary sharply. Such models are also necessary to advise fishery managers on how and when global warming projections of the IPCC model ensemble should be factored into regulatory decisions. Specifically, we demonstrate that the annual timing of marine exit of Yukon River Chinook salmon (Oncorhynchus tshawytscha) at 63°N 165°W for 1961–2009 varied in close concert with modelled sea surface temperature, air temperature, and sea ice cover. The best linear model for 1961–2009 combines sea surface and air temperatures to explain 59% of the annual variability in migratory timing (ice cover is available only for 1970–2009). Changes in phenology of high-latitude Chinook salmon are expected in response to global warming. As average temperatures increase, the frequency of earlier migrations is expected to increase, making management of the fishery more challenging.
Genetic Characterization of Measles Vaccine Strains
Authors: Bankamp Bettina , Takeda Makoto , Zhang Yan , Xu Wenbo , Rota Paul A.
Published: June 2011

The complete genomic sequences of 9 measles vaccine strains were compared with the sequence of the Edmonston wild-type virus. AIK-C, Moraten, Rubeovax, Schwarz, and Zagreb are vaccine strains of the Edmonston lineage, whereas CAM-70, Changchun-47, Leningrad-4 and Shanghai-191 were derived from 4 different wild-type isolates. Nucleotide substitutions were found in the noncoding regions of the genomes as well as in all coding regions, leading to deduced amino acid substitutions in all 8 viral proteins. Although the precise mechanisms involved in the attenuation of individual measles vaccines remain to be elucidated, in vitro assays of viral protein functions and recombinant viruses with defined genetic modifications have been used to characterize the differences between vaccine and wild-type strains. Although almost every protein contributes to an attenuated phenotype, substitutions affecting host cell tropism, virus assembly, and the ability to inhibit cellular antiviral defense mechanisms play an especially important role in attenuation.
Intensive care unit discharge to the ward with a tracheostomy cannula as a risk factor for mortality: A prospective, multicenter propensity analysis*
Authors: Fernandez Rafael , Tizon Ana-Isabel , Gonzalez Javier , Monedero Pablo , Garcia-Sanchez Manuela , de-la-Torre Ma-Victoria , Ibañez Pedro , Frutos Fernando , del-Nogal Frutos , Gomez Ma-Jesus , Marcos Alfredo , Hernández Gonzalo
Published: June 2011

Objective:

To analyze the impact of decannulation before intensive care unit discharge on ward survival in nonexperimental conditions.

Design:

Prospective, observational survey.

Setting:

Thirty-one intensive care units throughout Spain.

Patients:

All patients admitted from March 1, 2008 to May 31, 2008.

Interventions:

None.

Measurements and Main Results:

At intensive care unit discharge, we recorded demographic variables, severity score, and intensive care unit treatments, with special attention to tracheostomy. After intensive care unit discharge, we recorded intensive care unit readmission and hospital survival. Statistics: Multivariate analyses for ward mortality, with Cox proportional hazard ratio adjusted for propensity score for intensive care unit decannulation. We included 4,132 patients, 1,996 of whom needed mechanical ventilation. Of these, 260 (13%) were tracheostomized and 59 (23%) died in the intensive care unit. Of the 201 intensive care unit tracheostomized survivors, 60 were decannulated in the intensive care unit and 141 were discharged to the ward with cannulae in place. Variables associated with intensive care unit decannulation (non-neurologic disease [85% vs. 64%], vasoactive drugs [90% vs. 76%], parenteral nutrition [55% vs. 33%], acute renal failure [37% vs. 23%], and good prognosis at intensive care unit discharge [40% vs. 18%]) were included in a propensity score model for decannulation. Crude ward mortality was similar in decannulated and nondecannulated patients (22% vs. 23%); however, after adjustment for the propensity score and Sabadell Score, the presence of a tracheostomy cannula was not associated with any survival disadvantage with an odds ratio of 0.6 [0.3–1.2] (p = .1).

Conclusion:

In our multicenter setting, intensive care unit discharge before decannulation is not a risk factor.
On the inference of function from structure using biomechanical modelling and simulation of extinct organisms
Authors: Hutchinson John R.
Published: June 2011

Biomechanical modelling and simulation techniques offer some hope for unravelling the complex inter-relationships of structure and function perhaps even for extinct organisms, but have their limitations owing to this complexity and the many unknown parameters for fossil taxa. Validation and sensitivity analysis are two indispensable approaches for quantifying the accuracy and reliability of such models or simulations. But there are other subtleties in biomechanical modelling that include investigator judgements about the level of simplicity versus complexity in model design or how uncertainty and subjectivity are dealt with. Furthermore, investigator attitudes toward models encompass a broad spectrum between extreme credulity and nihilism, influencing how modelling is conducted and perceived. Fundamentally, more data and more testing of methodology are required for the field to mature and build confidence in its inferences.
Genome-wide detection of novel regulatory RNAs in E. coli
Authors: Raghavan Rahul , Groisman Eduardo A. , Ochman Howard
Published: June 2011

The intergenic regions in bacterial genomes can contain regulatory leader sequences and small RNAs (sRNAs), which both serve to modulate gene expression. Computational analyses have predicted the presence of hundreds of these noncoding regulatory RNAs in Escherichia coli; however, only about 80 have been experimentally validated. By applying a deep-sequencing approach, we detected and quantified the vast majority of the previously validated regulatory elements and identified 10 new sRNAs and nine new regulatory leader sequences in the intergenic regions of E. coli. Half of the newly discovered sRNAs displayed enhanced stability in the presence of the RNA-binding protein Hfq, which is vital to the function of many of the known E. coli sRNAs. Whereas previous methods have often relied on phylogenetic conservation to identify regulatory leader sequences, only five of the newly discovered E. coli leader sequences were present in the genomes of other enteric species. For those newly identified regulatory elements having orthologs in Salmonella, evolutionary analyses showed that these regions encoded new noncoding elements rather than small, unannotated protein-coding transcripts. In addition to discovering new noncoding regulatory elements, we validated 53 sRNAs that were previously predicted but never detected and showed that the presence, within intergenic regions, of σ70 promoters and sequences with compensatory mutations that maintain stable RNA secondary structures across related species is a good predictor of novel sRNAs.
Cactus: Algorithms for genome multiple sequence alignment
Authors: Paten Benedict , Earl Dent , Nguyen Ngan , Diekhans Mark , Zerbino Daniel , Haussler David
Published: June 2011

Much attention has been given to the problem of creating reliable multiple sequence alignments in a model incorporating substitutions, insertions, and deletions. Far less attention has been paid to the problem of optimizing alignments in the presence of more general rearrangement and copy number variation. Using Cactus graphs, recently introduced for representing sequence alignments, we describe two complementary algorithms for creating genomic alignments. We have implemented these algorithms in the new “Cactus” alignment program. We test Cactus using the Evolver genome evolution simulator, a comprehensive new tool for simulation, and show using these and existing simulations that Cactus significantly outperforms all of its peers. Finally, we make an empirical assessment of Cactus's ability to properly align genes and find interesting cases of intra-gene duplication within the primates.
Cytokinin Interplay with Ethylene, Auxin, and Glucose Signaling Controls Arabidopsis Seedling Root Directional Growth
Authors: Kushwah Sunita , Jones Alan M. , Laxmi Ashverya
Published: June 2011

Optimal root architecture is established by multiple intrinsic (e.g. hormones) and extrinsic (e.g. gravity and touch) signals and is established, in part, by directed root growth. We show that asymmetrical exposure of cytokinin (CK) at the root tip in Arabidopsis (Arabidopsis thaliana) promotes cell elongation that is potentiated by glucose in a hexokinase-influenced, G protein-independent manner. This mode of CK signaling requires the CK receptor, ARABIDOPSIS HISTIDINE KINASE4 and, at a minimum, its cognate type B ARABIDOPSIS RESPONSE REGULATORS ARR1, ARR10, and ARR11 for full responsiveness, while type A response regulators act redundantly to attenuate this CK response. Ethylene signaling through the ethylene receptor ETHYLENE RESISTANT1 and its downstream signaling element ETHYLENE INSENSITIVE2 are required for CK-induced root cell elongation. Negative and positive feedback loops are reinforced by CK regulation of the expression of the genes encoding these elements in both the CK and ethylene signaling pathways. Auxin transport facilitated by PIN-FORMED2 as well as auxin signaling through control of the steady-state level of transcriptional repressors INDOLE-3-ACETIC ACID7 (IAA7), IAA14, and IAA17 via TRANSPORT INHIBITOR RESPONSE1/AUXIN SIGNALING F-BOX PROTEIN are involved in CK-induced root cell elongation. This action lies downstream of ethylene and CK induction. Intrinsic signaling in this response operates independently of the extrinsic signal touch, although actin filament organization, which is important in the touch response, may be important for this response, since latrunculin B can induce similar growth. This root growth response may have adaptive significance, since CK responsiveness is inversely related to root coiling and waving, two root behaviors known to be important for fitness.
Sphingolipids Containing Very-Long-Chain Fatty Acids Define a Secretory Pathway for Specific Polar Plasma Membrane Protein Targeting inArabidopsis
Authors: Markham Jennifer E. , Molino Diana , Gissot Lionel , Bellec Yannick , Hématy Kian , Marion Jessica , Belcram Katia , Palauqui Jean-Christophe , Satiat-JeuneMaître Béatrice , Faure Jean-Denis
Published: June 2011

Sphingolipids are a class of structural membrane lipids involved in membrane trafficking and cell polarity. Functional analysis of the ceramide synthase family in Arabidopsis thaliana demonstrates the existence of two activities selective for the length of the acyl chains. Very-long-acyl-chain (C > 18 carbons) but not long-chain sphingolipids are essential for plant development. Reduction of very-long-chain fatty acid sphingolipid levels leads in particular to auxin-dependent inhibition of lateral root emergence that is associated with selective aggregation of the plasma membrane auxin carriers AUX1 and PIN1 in the cytosol. Defective targeting of polar auxin carriers is characterized by specific aggregation of Rab-A2a– and Rab-A1e–labeled early endosomes along the secretory pathway. These aggregates correlate with the accumulation of membrane structures and vesicle fragmentation in the cytosol. In conclusion, sphingolipids with very long acyl chains define a trafficking pathway with specific endomembrane compartments and polar auxin transport protein cargoes.
Botrytis cinerea Manipulates the Antagonistic Effects between Immune Pathways to Promote Disease Development in Tomato
Authors: El Oirdi Mohamed , El Rahman Taha Abd , Rigano Luciano , El Hadrami Abdelbasset , Rodriguez María Cecilia , Daayf Fouad , Vojnov Adrian , Bouarab Kamal
Published: June 2011

Plants have evolved sophisticated mechanisms to sense and respond to pathogen attacks. Resistance against necrotrophic pathogens generally requires the activation of the jasmonic acid (JA) signaling pathway, whereas the salicylic acid (SA) signaling pathway is mainly activated against biotrophic pathogens. SA can antagonize JA signaling and vice versa. Here, we report that the necrotrophic pathogen Botrytis cinerea exploits this antagonism as a strategy to cause disease development. We show that B. cinerea produces an exopolysaccharide, which acts as an elicitor of the SA pathway. In turn, the SA pathway antagonizes the JA signaling pathway, thereby allowing the fungus to develop its disease in tomato (Solanum lycopersicum). SA-promoted disease development occurs through Nonexpressed Pathogen Related1. We also show that the JA signaling pathway required for tomato resistance against B. cinerea is mediated by the systemin elicitor. These data highlight a new strategy used by B. cinerea to overcome the plant's defense system and to spread within the host.
A Guideline to Family-Wide Comparative State-of-the-Art Quantitative RT-PCR Analysis Exemplified with a Brassicaceae Cross-Species Seed Germination Case Study
Authors: Graeber Kai , Linkies Ada , Wood Andrew T.A. , Leubner-Metzger Gerhard
Published: June 2011

Comparative biology includes the comparison of transcriptome and quantitative real-time RT-PCR (qRT-PCR) data sets in a range of species to detect evolutionarily conserved and divergent processes. Transcript abundance analysis of target genes by qRT-PCR requires a highly accurate and robust workflow. This includes reference genes with high expression stability (i.e., low intersample transcript abundance variation) for correct target gene normalization. Cross-species qRT-PCR for proper comparative transcript quantification requires reference genes suitable for different species. We addressed this issue using tissue-specific transcriptome data sets of germinating Lepidium sativum seeds to identify new candidate reference genes. We investigated their expression stability in germinating seeds of L.  sativum and Arabidopsis thaliana by qRT-PCR, combined with in silico analysis of Arabidopsis and Brassica napus microarray data sets. This revealed that reference gene expression stability is higher for a given developmental process between distinct species than for distinct developmental processes within a given single species. The identified superior cross-species reference genes may be used for family-wide comparative qRT-PCR analysis of Brassicaceae seed germination. Furthermore, using germinating seeds, we exemplify optimization of the qRT-PCR workflow for challenging tissues regarding RNA quality, transcript stability, and tissue abundance. Our work therefore can serve as a guideline for moving beyond Arabidopsis by establishing high-quality cross-species qRT-PCR.
Tunable Membrane Binding of the Intrinsically Disordered Dehydrin Lti30, a Cold-Induced Plant Stress Protein
Authors: Eriksson Sylvia K. , Kutzer Michael , Procek Jan , Gröbner Gerhard , Harryson Pia
Published: June 2011

Dehydrins are intrinsically disordered plant proteins whose expression is upregulated under conditions of desiccation and cold stress. Their molecular function in ensuring plant survival is not yet known, but several studies suggest their involvement in membrane stabilization. The dehydrins are characterized by a broad repertoire of conserved and repetitive sequences, out of which the archetypical K-segment has been implicated in membrane binding. To elucidate the molecular mechanism of these K-segments, we examined the interaction between lipid membranes and a dehydrin with a basic functional sequence composition: Lti30, comprising only K-segments. Our results show that Lti30 interacts electrostatically with vesicles of both zwitterionic (phosphatidyl choline) and negatively charged phospholipids (phosphatidyl glycerol, phosphatidyl serine, and phosphatidic acid) with a stronger binding to membranes with high negative surface potential. The membrane interaction lowers the temperature of the main lipid phase transition, consistent with Lti30's proposed role in cold tolerance. Moreover, the membrane binding promotes the assembly of lipid vesicles into large and easily distinguishable aggregates. Using these aggregates as binding markers, we identify three factors that regulate the lipid interaction of Lti30 in vitro: (1) a pH dependent His on/off switch, (2) phosphorylation by protein kinase C, and (3) reversal of membrane binding by proteolytic digest.
Gimeracil, an inhibitor of dihydropyrimidine dehydrogenase, inhibits the early step in homologous recombination
Authors: Sakata Koh‐Ichi , Someya Masanori , Matsumoto Yoshihisa , Tauchi Hiroshi , Kai Masahiro , Toyota Minoru , Takagi Masaru , Hareyama Masato , Fukushima Masakazu
Published: June 2011

Gimeracil (5‐chloro‐2, 4‐dihydroxypyridine) is an inhibitor of dihydropyrimidine dehydrogenase (DPYD), which degrades pyrimidine including 5‐fluorouracil in the blood. Gimeracil was originally added to an oral fluoropyrimidine derivative S‐1 to yield prolonged 5‐fluorouracil concentrations in serum and tumor tissues. We have already reported that gimeracil had radiosensitizing effects by partially inhibiting homologous recombination (HR) in the repair of DNA double strand breaks. We investigated the mechanisms of gimeracil radiosensitization. Comet assay and radiation‐induced focus formation of various kinds of proteins involved in HR was carried out. siRNA for DPYD were transfected to HeLa cells to investigate the target protein for radiosensitization with gimeracil. SCneo assay was carried out to examine whether DPYD depletion by siRNA inhibited HR repair of DNA double strand breaks. Tail moments in neutral comet assay increased in gimeracil‐treated cells. Gimeracil restrained the formation of foci of Rad51 and replication protein A (RPA), whereas it increased the number of foci of Nbs1, Mre11, Rad50, and FancD2. When HeLa cells were transfected with the DPYD siRNA before irradiation, the cells became more radiosensitive. The degree of radiosensitization by transfection of DPYD siRNA was similar to that of gimeracil. Gimeracil did not sensitize DPYD‐depleted cells. Depletion of DPYD by siRNA significantly reduced the frequency of neopositive clones in SCneo assay. Gimeracil partially inhibits the early step in HR. It was found that DPYD is the target protein for radiosensitization by gimeracil. The inhibitors of DPYD, such as gimeracil, could enhance the efficacy of radiotherapy through partial suppression of HR‐mediated DNA repair. (Cancer Sci 2011; 102: 1712–1716)
Downregulation of Cockayne syndrome B protein reduces human 8‐oxoguanine DNA glycosylase‐1 expression and repair of UV radiation‐induced 8‐oxo‐7,8‐dihydro‐2′‐deoxyguanine
Authors: Javeri Arash , Guy Lyons James , Huang Xiao X. , Halliday Gary M.
Published: June 2011

Human 8‐oxoguanine DNA glycosylase‐1 (hOGG1) is the key DNA repair enzyme responsible for initiating repair of UV radiation‐induced 8‐oxo‐7,8‐dihydro‐2′‐deoxyguanosine (8‐oxo‐dG). Previously we have shown that basal cells in human epidermis are particularly sensitive to UVA‐mediated DNA damage probably due to low expression of hOGG1. Here we investigate some aspects of the regulatory role of Cockayne syndrome B (CSB) on hOGG1 expression and function. Cockayne syndrome B and hOGG1 genes were knocked down by miRNA technology in the HaCaT human keratinocyte cell line. Loss of the CSB gene decreased hOGG1 mRNA, and loss of hOGG1 increased CSB, indicating that they influence each other’s expression. Protein levels were assessed in cells grown into engineered human skin using immunohistochemistry. This confirmed that CSB knockdown with miRNA reduced hOGG1 protein levels, but hOGG1 knockdown did not influence expression of CSB protein. Using comet assay we found that both hOGG1 and CSB knockdown reduced repair of both UVA‐ and UVB‐induced 8‐oxo‐dG, consistent with CSB downregulation of hOGG1 mRNA and protein. In contrast, CSB but not hOGG1 knockdown reduced repair of UVB‐ and UVA‐induced cyclobutane pyrimidine dimer photolesions. In engineered human skin, repair of UVA‐induced 8‐oxo‐dG was inhibited by both hOGG1 and CSB knockdown, confirming the functional role of both proteins in cells with 3‐D cellular contacts. These findings directly indicate that hOGG1 and CSB influence each other’s expression. CSB is required for maintaining hOGG1 enzyme levels and function. Cockayne syndrome B could therefore be required for 8‐oxo‐dG repair due to its regulatory effect on hOGG1 expression. Cockayne syndrome B but not hOGG1 is also required for efficient repair of cyclobutane pyrimidine dimers. Cockayne syndrome B regulation of DNA repair could contribute to the effect of UVA in causing mutations that lead to skin cancer in humans. (Cancer Sci 2011; 102: 1651–1658)
Genetic ablation of a candidate tumor suppressor gene, Rest, does not promote mouse colon carcinogenesis
Authors: Hatano Yuichiro , Yamada Yasuhiro , Hata Kazuya , Phutthaphadoong Suphot , Aoki Hitomi , Hara Akira
Published: June 2011

Colon carcinogenesis is a multistage process involving genetic alterations of various tumor suppressor genes and oncogenes. Repressor element 1 silencing factor (REST ), which was originally discovered as a transcriptional repressor of neuronal genes, plays an important role in neuronal differentiation. In a previous genetic screening for tumor suppressor genes in human cancers, REST was identified as a candidate tumor suppressor gene in colorectal carcinogenesis. However, the role of Rest in colon carcinogenesis in vivo remains unclear because of the embryonic lethal phenotype of the conventional Rest knockout mouse. In the present study, we conditionally deleted the Rest gene in the intestinal epithelium and investigated the effect of Rest ablation in mouse colon tumorigenesis. A conditional ablation of Rest in the colonic crypts led to a rapid upregulation of Rest‐targeted genes, such as Syt4, Bdnf, and Tubb3, suggesting that Rest actually suppresses the expression of its target genes in the colon. However, Rest ablation did not lead to any significant effect on the development of colon tumors in two independent mouse models of colon carcinogenesis. In addition, despite the upregulation of neuronal genes in the colonic crypts, no neuronal differentiation was observed in the colonic crypts and tumors after the Rest ablation. These results indicate that the loss of Rest expression by itself does not promote the development of colon tumors in mice, and suggest that REST may exert a tumor suppressing activity in conjunction with the additional genetic/epigenetic abnormalities that occur during colon carcinogenesis. (Cancer Sci 2011; 102: 1659–1664)
Systematic exploration of cancer‐associated microRNA through functional screening assays
Authors: Izumiya Masashi , Tsuchiya Naoto , Okamoto Koji , Nakagama Hitoshi
Published: June 2011

MicroRNA (miRNA), non‐coding RNA of approximately 22 nucleotides, post‐transcriptionally represses expression of its target genes. miRNA regulates a variety of biological processes such as cell proliferation, cell death, development, stemness and genomic stability, not only in physiological conditions but also in various pathological conditions such as cancers. More than 1000 mature miRNA have been experimentally identified in humans and mice, yet the functions of a vast majority of miRNA remain to be elucidated. Identification of novel cancer‐associated miRNA seems promising considering their possible application in the development of novel cancer therapies and biomarkers. Currently, there are two major approaches to identify miRNA that are associated with cancer: expression profiling study and functional screening assay. The former approach is widely used, and a large number of studies have shown aberrant miRNA expression profiles in cancer tissues compared with their non‐cancer counterparts. Although aberrantly expressed miRNA are potentially good biomarkers, in most cases a majority of them do not play causal roles in cancers when functional assays are performed. In contrast, the latter approach allows screening of ‘driver’ miRNA with cancer‐associated phenotypes, such as cell proliferation and cell invasion. Thus, this approach might be suitable in finding crucial targets of novel cancer therapy. The combination of both types of approaches will contribute to further elucidation of the cancer pathophysiology and to the development of a novel class of cancer therapies and biomarkers. (Cancer Sci 2011; 102: 1615–1621)
NF‐κB is activated in oesophageal fibroblasts in response to a paracrine signal generated by acid‐exposed primary oesophageal squamous cells
Authors: Green Nicola H. , Huang Qizhi , Corfe Bernard M. , Bury Jonathan P. , MacNeil Sheila
Published: June 2011

Oesophageal exposure to duodenogastro‐oesophageal refluxate leads to reflux oesophagitis and is implicated in the development of Barrett’s metaplasia (BM). NF‐κB signalling in epithelial cells is associated with the activation of transcription factors believed to be central to BM development, whilst NF‐κB activation in fibroblasts plays a critical role in matrix remodelling. Our aim was to study the effects of acid exposure on NF‐κB activation in primary human oesophageal fibroblasts (HOFs) and primary and immortalized oesophageal squames and to investigate any epithelial/stromal interactions in the response of these cells to acid. Primary HOFs and primary and immortalized oesophageal epithelial cells were exposed to acid (pH 7 – pH 4 ≤ 120 min) in single or pulsed treatments. Conditioned medium from epithelial cells following acid exposure was also applied to fibroblasts. Cell viability was determined by MTT‐ESTA. NF‐κB activation was determined by cellular localization of NF‐κB/p65 visualized by immunofluorescence. Conditioned medium from oesophageal epithelial cells, subjected to pH 5 pulsatile exposure, activated NF‐κB in fibroblasts, with some inter‐patient variability, but these conditions did not directly activate NF‐κB in the epithelial cells themselves. Significant NF‐κB activation was seen in the epithelial cells but only with greater acidity and exposure times (pH 4, 60–120 min). Our findings show that acid exposure can cause indirect activation of stromal cells by epithelial–stromal interactions. This may contribute to the pathogenesis of oesophageal diseases, and the inter‐patient variability may go some way to explain why some patients with reflux oesophagitis develop BM and others do not.