bluuebunny/crossref_metadata_2025 huggingface dataset:
Scatterer induced mode splitting in poly(dimethylsiloxane) coated microresonators
Authors: He Lina , Ozdemir Sahin Kaya , Zhu Jiangang , Yang Lan
Published: June 2010

We investigate scatterer induced mode splitting in a composite microtoroidal resonator (Q∼106) fabricated by coating a silica microtoroid (Q∼107) with a thin poly(dimethylsiloxane) layer. We show that the two split modes in both coated and uncoated silica microtoroids respond in the same way to the changes in the environmental temperature. This provides a self-referencing scheme which is robust to temperature perturbations. Together with the versatile functionalities of polymer materials, mode splitting in polymer and polymer coated microresonators offers an attractive sensing platform that is robust to thermal noise.
Nonuniformity of a planar polarizer for spin-transfer-induced vortex oscillations at zero field
Authors: Khvalkovskiy A. V. , Grollier J. , Locatelli N. , Gorbunov Ya. V. , Zvezdin K. A. , Cros V.
Published: June 2010

We discuss a possible mechanism of the spin-transfer-induced oscillations of a vortex in the free layer of spin-valve nanostructures, in which the polarizer layer has a planar magnetization. We demonstrate that if such planar polarizer is essentially nonuniform, steady gyrotropic vortex motion with large amplitude can be excited. The best excitation efficiency is obtained for a circular magnetization distribution in the polarizer. In this configuration, the conditions for the onset of the oscillations depend on the vortex chirality but not on the direction of its core.
Enhanced exchange anisotropy in IrMn/CoFeB systems and its correlation with uncompensated interfacial spins
Authors: Du Yuqing , Pan Genhua , Moate Roy , Ohldag Hendrik , Kovacs Andras , Kohn Amit
Published: June 2010

Bottom pinned exchange bias systems of IrMn/CoFe and IrMn/CoFeB on CoFe seed layers were studied. Enhanced exchange anisotropy has been observed for IrMn/CoFeB samples annealed at 350 °C. The ferromagnetic and antiferromagnetic layers of both samples are polycrystalline and textured {110} for the CoFe and CoFeB, and {111} for IrMn. Results demonstrated that the enhanced exchange anisotropy in the IrMn/CoFeB system is closely associated with the increased uncompensated interfacial spins as evidenced by the enhanced Mn x-ray magnetic circular dichroism (XMCD) signal strength. A quantitative correlation between the Mn XMCD signal and the exchange anisotropy constant Jk was observed.
Exponentially fitted open Newton–Cotes differential methods as multilayer symplectic integrators
Authors: Vanden Berghe G. , Van Daele M.
Published: June 2010

Classical open and closed Newton–Cotes differential methods possessing the characteristics of multilayer symplectic structures have been constructed in the past. In this paper, we study the exponentially fitted open Newton–Cotes differential methods of order two, four, and six. It is shown that these integrators, just as their classical counterparts, preserve the volume in the phase space of a Hamiltonian system. They can be converted into a multilayer symplectic structure so that volume-preserving integrators of a Hamiltonian system are obtained. A numerical example has been carried out to show the effectiveness of the present differential method.
Morphology characterization of argon-mediated epitaxial graphene on C-face SiC
Authors: Tedesco J. L. , Jernigan G. G. , Culbertson J. C. , Hite J. K. , Yang Y. , Daniels K. M. , Myers-Ward R. L. , Eddy C. R. , Robinson J. A. , Trumbull K. A. , Wetherington M. T. , Campbell P. M. , Gaskill D. K.
Published: June 2010

Epitaxial graphene layers were grown on the C-face of 4H–SiC and 6H–SiC using an argon-mediated growth process. Variations in growth temperature and pressure were found to dramatically affect the morphological properties of the layers. The presence of argon during growth slowed the rate of graphene formation on the C-face and led to the observation of islanding. The similarity in the morphology of the islands and continuous films indicated that island nucleation and coalescence is the growth mechanism for C-face graphene.
Strong coupling in a quantum dot micropillar system under electrical current injection
Authors: Kistner C. , Morgener K. , Reitzenstein S. , Schneider C. , Höfling S. , Worschech L. , Forchel A. , Yao P. , Hughes S.
Published: June 2010

Integrating In0.3Ga0.7As quantum dots (QDs) featuring a high oscillator strength into a high quality electrically contacted micropillar cavity enabled us to realize strong coupling under electrical carrier injection. In the micropillar cavity with a quality factor of 10 000 and a diameter of 1.9 μm, a vacuum Rabi splitting of 108 μeV was observed when an electrically excited QD exciton was tuned through resonance with the fundamental cavity mode by varying the temperature.
High-energy-density physics
Authors: Drake R. Paul
Published: June 2010

The novel, mysterious, and controversial behavior of matter at high pressure involves the interplay of electromagnetic, statistical, quantum, and relativistic physics.
Magnetic field reconnection: A first-principles perspective
Authors: Mozer Forrest S. , Pritchett Philip L.
Published: June 2010

Recent satellite missions and computer simulations of charged-particle dynamics in Earth’s magnetosphere are helping unravel the mysteries behind the breaking and reforming of magnetic field lines and the concomitant acceleration of electrons to high energies.
Heavy Element Abundances in Planetary Nebulae: A Theorist's Perspective
Authors: Karakas Amanda I. , Lugaro Maria
Published: May 2010

The determination of heavy element abundances from planetary nebula (PN) spectra provides an exciting opportunity to study the nucleosynthesis occurring in the progenitor asymptotic giant branch (AGB) star. We perform post-processing calculations on AGB models of a large range of mass and metallicity to obtain predictions for the production of neutron-capture elements up to the first s-process peak at strontium. We find that solar metallicity intermediate-mass AGB models provide a reasonable match to the heavy element composition of Type I PNe. Likewise, many of the Se and Kr enriched PNe are well fitted by lower mass models with solar or close-to-solar metallicities. However, those objects most enriched in Krand those PN with sub-solar Se/O ratios are difficult to explain with AGB-nucleosynthesis models. Furthermore, we compute s-process abundance predictions for low-mass AGB models of very low metallicity ([Fe/H]≈−2.3) using both scaled solar and an α-enhanced initial composition. For these models, O is dredged to the surface, which means that abundance ratios measured relative to this element (e.g. X/O) do not provide a reliable measure of initial abundance ratios, or of production within the star owing to internal nucleosynthesis.
Sub-Arcsecond Morphology of Planetary Nebulae
Authors: Miranda L. F. , Ramos-Larios G. , Guerrero M. A.
Published: May 2010

Planetary nebulae (PNe) can be roughly categorized into several broad morphological classes. The high quality images of PNe acquired in recent years, however, have revealed a wealth of fine structures that preclude simplistic models for their formation. Here we present narrow-band, sub-arcsecond images of a sample of relatively large PNe that illustrate the complexity and variety of small-scale structures. This is especially true for bipolar PNe, for which the images reveal multi-polar ejections and, in some cases, suggest turbulent gas motions. Our images also reveal the presence or signs of jet-like outflows in several objects in which this kind of component has not been previously reported.
High-Resolution Spectroscopy of the Planetary Nebulae PM 1–242, PM 1–318 and PM 1–322
Authors: Miranda L. F. , Vázquez R. , Guerrero M. A. , Pereira C. B. , Iñiguez-Garín E.
Published: May 2010

We have recently confirmed the planetary nebula (PN) nature of PM 1–242, PM 1–318 and PM 1–322. Here we present high-resolution long-slit spectra of these three PNe in order to analyze their internal kinematics and to investigate their physical structure. PM 1–242 is a tilted ring and not an elliptical PN as suggested by direct images. The object is probably related to ring-like PNe and shows an unusual pointsymmetric brightness distribution in the ring. PM 1–318 is a pole-on elliptical PN, instead of a circular one as suggested by direct images. PM 1–322 is spatially unresolved and its spectrum shows large differences between the forbidden lines and Hα profiles, with the latter showing a double-peaked profile and relatively extended wings (FWZI ~325 km s−1). These properties are found in other PNe that are suspected to host a symbiotic central star.
Legacies of the Macquarie/AAO/Strasbourg Hα Planetary Nebula Project (MASH): An International Workshop in Honour of the Career of Agnès Acker
Authors: Parker Quentin A.
Published: May 2010

A concise summary of the recent international workshop held in honour of the career of Agnès Acker is presented together with a brief exposition of her productive career in the study of Planetary Nebulae, the expelled, ionised outer shrouds of dying stars.
Planetary Nebulae: Observational Properties, Mimics and Diagnostics
Authors: Frew David J. , Parker Quentin A.
Published: May 2010

The total number of true, likely and possible planetary nebulae (PN) now known in the Milky Way is nearly 3000, double the number known a decade ago. The new discoveries are a legacy of the recent availability of wide field, narrowband imaging surveys, primarily in the light of H-alpha. In this paper, we summarise the various PN discovery techniques, and give an overview of the many types of objects which mimic PN and which appear as contaminants in both Galactic and extragalactic samples. Much improved discrimination of classical PN from their mimics is now possible based on the wide variety of high-quality multiwavelength data sets that are now available. We offer improved taxonomic and observational definitions for the PN phenomenon based on evaluation of these better diagnostic capabilities. However, we note that evidence is increasing that the PN phenomenon is heterogeneous, and PN are likely to be formed from multiple evolutionary scenarios. In particular, the relationships between some collimated symbiotic outflows and bipolar PN remain uncertain.
An Evaluation of the Excitation-Class Parameter for the Central Stars of Planetary Nebulae
Authors: Reid Warren A. , Parker Quentin A.
Published: May 2010

The three main methods currently in use for estimating the excitation class of planetary nebulae (PNe) central stars are compared and evaluated using 586 newly discovered and previously known PNe in the Large Magellanic Cloud (LMC). In order to achieve this we ran a series of evaluation tests using line ratios derived from de-reddened, flux-calibrated spectra. Pronounced differences between the methods are exposed after comparing the distribution of objects to their derived excitation. Line ratio comparisons show that each method's input parameters have a strong effect on the estimated excitation of a central star. Diagrams were created by comparing excitation classes with Hβ line fluxes. The best methods are then compared to published temperatures using the Zanstra method and assessed for their ability to reflect central star effective temperatures and evolution. As a result we call for a clarification of the term ‘excitation class’ according to the different input parameters used. The first method, which we refer to as Exneb relies purely on the ratios of certain key emission lines. The second method, which we refer to as Ex* includes modeling to create a continuous variable and, for optically thick PNe in the Magellanic Clouds, is designed to relate more closely to intrinsic stellar parameters. The third method, we refer to as Ex[Oiii]/Hβ since the [Oiii]/Hβ ratio is used in isolation to other temperature diagnostics. Each of these methods is shown to have serious drawbacks when used as an indicator for central star temperature. Finally, we suggest a new method (Exρ) for estimating excitation class incorporating both the [Oiii]/Hβ and the HeII λ4686/Hβ ratios. Although any attempt to provide accurate central star temperatures using the excitation class derived from nebula lines will always be limited, we show that this new method provides a substantial improvement over previous methods with better agreement to temperatures derived through the Zanstra method.
Allelic diversity in a novel gene pool of canola-quality Brassica napus enriched with alleles from B. rapa and B. carinata
Authors: Chen S. , Zou J. , Cowling W. A. , Meng J.
Published: June 2010

Brassica napus is an amphidiploid with genome AACC and is relatively deficient in genetic diversity. The abundant genetic diversity in other A- and C-genome Brassica species is a valuable resource to expand the narrow gene pool of B. napus. Recently the Ar genomic components from Chinese B. rapa (ArAr) and Cc genomic components from Ethiopian mustard B. carinata (BBCcCc) were introgressed into B. napus through interspecific hybridisation, and the Ar/Cc components were enriched through two generations of molecular marker-assisted selection. In this study, the simple sequence repeat (SSR) allelic diversity of 29 of these new-type B. napus lines, 12 from the first generation and 17 from the second generation, was compared with 66 international B. napus varieties from Australia, China and other countries. Hierarchical clustering and two-dimensional multidimensional scaling revealed that second generation lines and a few first generation lines, all selected for high Ar/Cc components, formed a unique population that was distantly separated from international B. napus. This novel gene pool had significantly higher richness of private SSR alleles and more alleles per SSR marker than the international B. napus varieties. The new-type B. napus lines showed variation in agronomic traits beyond the canola-quality B. napus parent. Many of the lines had low erucic acid and low glucosinolates in the seed (canola quality), indicating that they could be utilised immediately in canola breeding programs.
Yield, yield components and shoot morphology of four contrasting lucerne (Medicago sativa) cultivars grown in three cool temperate environments
Authors: Pembleton K. G. , Donaghy D. J. , Volenec J. J. , Smith R. S. , Rawnsley R. P.
Published: June 2010

Understanding which component has the greatest influence on yield is vital when managing lucerne (Medicago sativa) crops to maximise the production of high-quality forage. However, both yield components and plant morphology are affected by interactions between environment conditions and plant genetics. Field experiments across three environments (dryland at Cambridge: 500 mm annual rainfall, brown sodosol soil type; dryland at Elliott: 1200 mm annual rainfall, red ferrosol soil type; and irrigated at Elliott) in Tasmania, Australia were undertaken to investigate the yield, yield components and plant morphology of four lucerne cultivars; DuPuits, Grasslands Kaituna, SARDI 7 and SARDI 10 under cutting. The effect of cultivar on dry matter (DM) yield was different in each environment, with Grasslands Kaituna achieving the highest yield (P < 0.05) in dryland environments, while no difference in DM yield among cultivars (P > 0.05) occurred under irrigation. Stepwise linear regression consistently confirmed mass per shoot as the yield component with the greatest influence on DM yield for all cultivars and environments. Shoot density also had an influence on DM yield in two of the three environments. DuPuits had the highest leaf : stem ratio in all three environments and slower morphological development in two of the environments. Management practices across all environments and cultivars should aim to increase mass per shoot to maximise yield. Of the cultivars examined Grasslands Kaituna is the most appropriate for dryland conditions in Tasmania, while all cultivars examined were suited to production under irrigation.
Laminin-based cell adhesion anchors microtubule plus ends to the epithelial cell basal cortex through LL5α/β
Authors: Hotta Azusa , Kawakatsu Tomomi , Nakatani Tomoya , Sato Toshitaka , Matsui Chiyuki , Sukezane Taiko , Akagi Tsuyoshi , Hamaji Tomoko , Grigoriev Ilya , Akhmanova Anna , Takai Yoshimi , Mimori-Kiyosue Yuko
Published: May 2010

LL5β has been identified as a microtubule-anchoring factor that attaches EB1/CLIP-associating protein (CLASP)–bound microtubule plus ends to the cell cortex. In this study, we show that LL5β and its homologue LL5α (LL5s) colocalize with autocrine laminin-5 and its receptors, integrins α3β1 and α6β4, at the basal side of fully polarized epithelial sheets. Depletion of both laminin receptor integrins abolishes the cortical localization of LL5s, whereas LL5 depletion reduces the amount of integrin α3 at the basal cell cortex. Activation of integrin α3 is sufficient to initiate LL5 accumulation at the cell cortex. LL5s form a complex with the cytoplasmic tails of these integrins, but their interaction might be indirect. Analysis of the three-dimensional distribution of microtubule growth by visualizing EB1-GFP in epithelial sheets in combination with RNA interference reveals that LL5s are required to maintain the density of growing microtubules selectively at the basal cortex. These findings reveal that signaling from laminin–integrin associations attaches microtubule plus ends to the epithelial basal cell cortex.
Innate immunity defines the capacity of antiviral T cells to limit persistent infection
Authors: Andrews Daniel M. , Estcourt Marie J. , Andoniou Christopher E. , Wikstrom Matthew E. , Khong Andrea , Voigt Valentina , Fleming Peter , Tabarias Hyacinth , Hill Geoffrey R. , van der Most Robbert G. , Scalzo Anthony A. , Smyth Mark J. , Degli-Esposti Mariapia A.
Published: June 2010

Effective immunity requires the coordinated activation of innate and adaptive immune responses. Natural killer (NK) cells are central innate immune effectors, but can also affect the generation of acquired immune responses to viruses and malignancies. How NK cells influence the efficacy of adaptive immunity, however, is poorly understood. Here, we show that NK cells negatively regulate the duration and effectiveness of virus-specific CD4+ and CD8+ T cell responses by limiting exposure of T cells to infected antigen-presenting cells. This impacts the quality of T cell responses and the ability to limit viral persistence. Our studies provide unexpected insights into novel interplays between innate and adaptive immune effectors, and define the critical requirements for efficient control of viral persistence.
Tob1 is a constitutively expressed repressor of liver regeneration
Authors: Ho Karen J. , Do Nhue L. , Otu Hasan H. , Dib Martin J. , Ren Xianghui , Enjyoji Keiichi , Robson Simon C. , Terwilliger Ernest F. , Karp Seth J.
Published: June 2010

How proliferative and inhibitory signals integrate to control liver regeneration remains poorly understood. A screen for antiproliferative factors repressed after liver injury identified transducer of ErbB2.1 (Tob1), a member of the PC3/BTG1 family of mito-inhibitory molecules as a target for further evaluation. Tob1 protein decreases after 2/3 hepatectomy in mice secondary to posttranscriptional mechanisms. Deletion of Tob1 increases hepatocyte proliferation and accelerates restoration of liver mass after hepatectomy. Down-regulation of Tob1 is required for normal liver regeneration, and Tob1 controls hepatocyte proliferation in a dose-dependent fashion. Tob1 associates directly with both Caf1 and cyclin-dependent kinase (Cdk) 1 and modulates Cdk1 kinase activity. In addition, Tob1 has significant effects on the transcription of critical cell cycle components, including E2F target genes and genes involved in p53 signaling. We provide direct evidence that levels of an inhibitory factor control the rate of liver regeneration, and we identify Tob1 as a crucial check point molecule that modulates the expression and activity of cell cycle proteins.
CisGenome Browser: a flexible tool for genomic data visualization
Authors: Jiang Hui , Wang Fan , Dyer Nigel P. , Wong Wing Hung
Published: June 2010

Summary: We present an open source, platform independent tool, called CisGenome Browser, which can work together with any other data analysis program to serve as a flexible component for genomic data visualization. It can also work by itself as a standalone genome browser. By working as a light-weight web server, CisGenome Browser is a convenient tool for data sharing between labs. It has features that are specifically designed for ultra high-throughput sequencing data visualization.

Availability:  http://biogibbs.stanford.edu/∼jiangh/browser/

Contact:  jiangh@stanford.edu
Reconsidering Japan's Underperformance in Pharmaceuticals: Evidence from Japan's Anticancer Drug Sector
Authors: Umemura Maki
Published: June 2010

Unlike its automobile or electronics industries, Japan's pharmaceutical industry did not become a global leader. Japan remains a net importer of pharmaceuticals and has introduced few global blockbuster drugs. Alfred Chandler argued that Japan's pharmaceutical firms remained relatively weak because Western firms enjoyed an insurmountable first first-mover advantage. However, this case study of the anticancer drug sector illustrates that Chandler's explanation is incomplete. Japanese medical culture, government policy, and research environment also played a substantial role in shaping the industry. In the 1970s and 1980s, these factors encouraged firms to develop little few effective drugs with low side effects, and profit from Japan's domestic market. But, these drugs were unsuitable to foreign markets with more demanding efficacy standards. As a result, Japan not only lost more than a decade in developing ineffective drugs, but also neglected to create the infrastructure necessary to develop innovative drugs and build a stronger pharmaceutical industry.
The potential impact of global warming on the efficacy of field margins sown for the conservation of bumble-bees
Authors: Memmott Jane , Carvell Claire , Pywell Richard F. , Craze Paul G.
Published: May 2010

Climate change is expected to drive species extinct by reducing their survival, reproduction and habitat. Less well appreciated is the possibility that climate change could cause extinction by changing the ecological interactions between species. If ecologists, land managers and policy makers are to manage farmland biodiversity sustainably under global climate change, they need to understand the ways in which species interact with each other as this will affect the way they respond to climate change. Here, we consider the ability of nectar flower mixtures used in field margins to provide sufficient forage for bumble-bees under future climate change. We simulated the effect of global warming on the network of plant–pollinator interactions in two types of field margin: a four-species pollen and nectar mix and a six-species wildflower mix. While periods without flowering resources and periods with no food were rare, curtailment of the field season was very common for the bumble-bees in both mixtures. The effect of this, however, could be ameliorated by adding extra species at the start and end of the flowering season. The plant species that could be used to future-proof margins against global warming are discussed.
Climate change and freshwater ecosystems: impacts across multiple levels of organization
Authors: Woodward Guy , Perkins Daniel M. , Brown Lee E.
Published: May 2010

Fresh waters are particularly vulnerable to climate change because (i) many species within these fragmented habitats have limited abilities to disperse as the environment changes; (ii) water temperature and availability are climate-dependent; and (iii) many systems are already exposed to numerous anthropogenic stressors. Most climate change studies to date have focused on individuals or species populations, rather than the higher levels of organization (i.e. communities, food webs, ecosystems). We propose that an understanding of the connections between these different levels, which are all ultimately based on individuals, can help to develop a more coherent theoretical framework based on metabolic scaling, foraging theory and ecological stoichiometry, to predict the ecological consequences of climate change. For instance, individual basal metabolic rate scales with body size (which also constrains food web structure and dynamics) and temperature (which determines many ecosystem processes and key aspects of foraging behaviour). In addition, increasing atmospheric CO2is predicted to alter molar CNP ratios of detrital inputs, which could lead to profound shifts in the stoichiometry of elemental fluxes between consumers and resources at the base of the food web. The different components of climate change (e.g. temperature, hydrology and atmospheric composition) not only affect multiple levels of biological organization, but they may also interact with the many other stressors to which fresh waters are exposed, and future research needs to address these potentially important synergies.
The role of YAP transcription coactivator in regulating stem cell self-renewal and differentiation
Authors: Lian Ian , Kim Joungmok , Okazawa Hideki , Zhao Jiagang , Zhao Bin , Yu Jindan , Chinnaiyan Arul , Israel Mason A. , Goldstein Lawrence S.B. , Abujarour Ramzey , Ding Sheng , Guan Kun-Liang
Published: June 2010

Yes-associated protein (YAP) is a potent transcription coactivator acting via binding to the TEAD transcription factor, and plays a critical role in organ size regulation. YAP is phosphorylated and inhibited by the Lats kinase, a key component of the Hippo tumor suppressor pathway. Elevated YAP protein levels and gene amplification have been implicated in human cancer. In this study, we report that YAP is inactivated during embryonic stem (ES) cell differentiation, as indicated by decreased protein levels and increased phosphorylation. Consistently, YAP is elevated during induced pluripotent stem (iPS) cell reprogramming. YAP knockdown leads to a loss of ES cell pluripotency, while ectopic expression of YAP prevents ES cell differentiation in vitro and maintains stem cell phenotypes even under differentiation conditions. Moreover, YAP binds directly to promoters of a large number of genes known to be important for stem cells and stimulates their expression. Our observations establish a critical role of YAP in maintaining stem cell pluripotency.
Emerging paradigms of regulated microRNA processing
Authors: Newman Martin A. , Hammond Scott M.
Published: June 2010

MicroRNAs (miRNAs) modulate a broad range of gene expression patterns during development and tissue homeostasis, and in the pathogenesis of disease. The exquisite spatio–temporal control of miRNA abundance is made possible, in part, by regulation of the miRNA biogenesis pathway. In this review, we discuss two emerging paradigms for post-transcriptional control of miRNA expression. One paradigm centers on the Microprocessor, the protein complex essential for maturation of canonical miRNAs. The second paradigm is specific to miRNA families, and requires interaction between RNA-binding proteins and cis-regulatory sequences within miRNA precursor loops.
MicroRNA-140 and the silencing of osteoarthritis
Authors: Araldi Elisa , Schipani Ernestina
Published: June 2010

MicroRNAs (miRNAs) have emerged as important modulators in development, tissue homeostasis, and diseases. In this issue of Genes & Development, Miyaki and colleagues (pp. 1173–1185) report that miR-140 is involved in the pathogenesis of osteoarthritis by regulating, at least in part, ADAMTS5. Moreover, mice lacking miR-140 are dwarf as a consequence of impaired chondrocyte proliferation. This study is the first in vivo demonstration that miR-140 has a critical and nonredundant role in cartilage development and homeostasis.
Purification of RNA by SDS Solubilization and Phenol Extraction
Authors: Rio Donald C. , Ares Manuel , Hannon Gregory J. , Nilsen Timothy W.
Published: June 2010

INTRODUCTION

This protocol describes a method for RNA purification by sodium dodecyl sulfate (SDS) solubilization and phenol extraction. It is of wide utility and is used routinely to deproteinize RNAs in biological material that has been solubilized in SDS, an ionic detergent that dissolves membranes, disrupts protein-nucleic acid interactions, and inactivates ribonucleases. Once solubilized, addition of phenol or phenol:chloroform:isoamyl alcohol (PCA) completely denatures the protein, and it becomes insoluble in aqueous solution. PCA extraction is the method of choice for preparing cytoplasmic RNA from tissue culture cells or in any other situation (e.g., enzyme reactions) where solubilization in SDS is easily achievable.
Removal of Ribosomal Subunits (and rRNA) from Cytoplasmic Extracts before Solubilization with SDS and Deproteinization
Authors: Rio Donald C. , Ares Manuel , Hannon Gregory J. , Nilsen Timothy W.
Published: June 2010

INTRODUCTION

More than 95% of total RNA is composed of ribosomal RNAs (rRNAs) (28S, 18S, 5.8S, and 5S). Here, we present a method that is effective in removing rRNA before extraction and purification of total RNA. If you choose to prepare cytoplasmic RNA and wish to analyze any RNA other than rRNA, it is desirable to eliminate the rRNAs by taking advantage of the fact that the ribosomal subunits are very large (40S and 60S). Few, if any, other cellular RNAs are present in such large macromolecular complexes. The vast majority of rRNAs can be removed by sedimentation. Of course, steps must be taken to avoid co-sedimentation of desired RNAs. Co-sedimentation can be greatly reduced by first dissociating ribosomes into their respective subunits by EDTA treatment. The subunits are then “cleaned” by treatment with high salt and nonionic detergent. Ribosomal subunits remain intact under these conditions and can be sedimented free of other RNAs. Subsequently, the remaining RNAs (messenger RNAs [mRNAs] and all other RNAs) can be purified and analyzed by a variety of methods.
Removal of DNA from RNA
Authors: Rio Donald C. , Ares Manuel , Hannon Gregory J. , Nilsen Timothy W.
Published: June 2010

INTRODUCTION

DNA contamination of RNA preparations can present significant problems, especially for polymerase chain reaction (PCR)-based applications. No RNA extraction procedure excludes DNA entirely. Cytoplasmic RNA can be contaminated with DNA because of nuclei breakage during preparation. Moreover, TRIzol preparations do not exclude plasmids or other small DNA fragments. This article describes the reliable and effective method of eliminating DNA from RNA preparations via DNase digestion. DNase I specifically digests DNA into small oligonucleotides, leaving RNA intact.
Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing
Authors: Meyer Matthias , Kircher Martin
Published: June 2010

INTRODUCTION

The large amount of DNA sequence data generated by high-throughput sequencing technologies often allows multiple samples to be sequenced in parallel on a single sequencing run. This is particularly true if subsets of the genome are studied rather than complete genomes. In recent years, target capture from sequencing libraries has largely replaced polymerase chain reaction (PCR) as the preferred method of target enrichment. Parallelizing target capture and sequencing for multiple samples requires the incorporation of sample-specific barcodes into sequencing libraries, which is necessary to trace back the sample source of each sequence. This protocol describes a fast and reliable method for the preparation of barcoded (“indexed”) sequencing libraries for Illumina’s Genome Analyzer platform. The protocol avoids expensive commercial library preparation kits and can be performed in a 96-well plate setup using multi-channel pipettes, requiring not more than two or three days of lab work. Libraries can be prepared from any type of double-stranded DNA, even if present in subnanogram quantity.
Tracking and Quantitative Analysis of Dynamic Movements of Cells and Particles
Authors: Rohr Karl , Godinez William J. , Harder Nathalie , Wörz Stefan , Mattes Julian , Tvaruskó Wolfgang , Eils Roland
Published: June 2010

INTRODUCTION

Understanding complex cellular processes requires investigating the underlying mechanisms within a spatiotemporal context. Although cellular processes are dynamic in nature, most studies in molecular cell biology are based on fixed specimens, for example, using immunocytochemistry or fluorescence in situ hybridization (FISH). However, breakthroughs in fluorescence microscopy imaging techniques, in particular, the discovery of green fluorescent protein (GFP) and its spectral variants, have facilitated the study of a wide range of dynamic processes by allowing nondestructive labeling of target structures in living cells. In addition, the tremendous improvements in spatial and temporal resolution of light microscopes now allow cellular processes to be analyzed in unprecedented detail. These state-of-the-art imaging technologies, however, provide a huge amount of digital image data. To cope with the enormous amount of image data and to extract reproducible as well as quantitative information, computer-based image analysis is required. In this article, we describe methods for computer-based analysis of multidimensional live cell microscopy images and their application to study the dynamics of cells and particles. First, we sketch a general workflow for quantitative analysis of live cell images. Then, we detail computational methods for automatic image analysis comprising image preprocessing, segmentation, registration, tracking, and classification. We conclude with a discussion of quantitative analysis and systems biology.
Meta-Analysis of Genome-Wide Association Studies
Authors: de Bakker Paul I.W. , Neale Benjamin M. , Daly Mark J.
Published: June 2010

INTRODUCTION

Individual genome-wide association studies have only limited power to find novel loci underlying complex traits and common diseases. With relatively modest sample and effect sizes, a true association between genotype and phenotype may never meet genome-wide statistical significance (P < 5 × 10-8) in a single study. Through meta-analysis, novel susceptibility loci can be discovered by effectively summing the statistical evidence of individually underpowered studies. Most genetic discoveries for complex traits are now made through meta-analysis collaborations, which so far have been restricted to single-locus analyses, testing for main effects at a single polymorphism at a time. A key benefit of this approach is that individual-level genotype (and phenotype) data do not need to be exchanged between research groups. In this article, we focus on meta-analysis at individual single-nucleotide polymorphisms (SNPs), paying particular attention to how imputation uncertainty can be incorporated into the association analysis and subsequent meta-analysis. Probably the most important aspect of genome-wide association meta-analysis is harmonization of the study results. As studies differ in design, sample collection, genotyping platforms, and association analysis methods, it is important that the association results (per SNP) of each study can be formatted, exchanged, and analyzed in such a way that the statistical evidence can be combined appropriately and that no valuable information is lost. Without minimizing the importance of having a clear phenotype definition (and corresponding measurements), we will assume that investigators representing the various studies have made sensible agreements about phenotype definitions, necessary sample exclusions, and appropriate covariate modeling.
Understanding Vulnerability and Resilience in the Context of Poverty and Ethnicity in Vietnam
Authors: Chi Truong Huyen
Published: June 2010

Based on ethnographic research among Kinh, Hmong and Cham H’Roi children in the highlands of Vietnam in 2008, this paper presents a narrative analysis of how poverty and ethnicity affect children’s experience of adversity. It explores the meanings children give to their experience and their use of discursive strategies such as criticising displays of wealth to create a repertoire of meanings from which personal and collective resilience is drawn. Acknowledging the ambiguities and contradictions in children’s accounts, the author reflects on how their understanding of social differences is underpinned by local power structures.
Shifting the Narrative: Child‐led Responses to Climate Change and Disasters in El Salvador and the Philippines
Authors: Tanner Thomas
Published: June 2010

Children and young people are commonly treated in the climate change and disasters literature as victims of natural events requiring protection by adults. This article critiques that narrative, drawing on examples from the Philippines and El Salvador that explore how children’s groups have responded to such issues through child‐centred initiatives. This highlights the importance of understanding children’s perception and communication of risks facing their lives and livelihoods, their potential as agents of change in preventing disasters and adapting to climate change, and the implications for the theory and practice of child participation, particularly in developing countries.
Clinical course of guttate psoriasis: Long‐term follow‐up study
Authors: KO Hyun‐Chang , JWA Seung‐Wook , SONG Margaret , KIM Moon‐Bum , KWON Kyung‐Sool
Published: June 2010

Guttate psoriasis, known to have a better prognosis than other types of psoriasis, shows rapid involution and longer remission, but its clinical course has barely been studied. The aim of this study was to determine the clinical course and to compare the clinical and laboratory features of guttate psoriasis. This is a retrospective study of 26 patients with guttate psoriasis. The patients were divided into two groups; the good one with complete remission and long remission for at least 1 year (group A) and the poor one with incomplete remission and progression into chronic plaque psoriasis (group B). Among 36 patients, 22 patients (61.1%) were group A and 14 patients (38.9%) were group B. In group A, most of the skin lesions disappeared within 8 months. In group B, two patients without proper treatment progressed to plaque psoriasis. The onset age was younger and more frequent upper respiratory infection and high anti‐streptolysin O (ASO) titer were found in group A, but family history of psoriasis was more common in group B. Patients had two distingushable clinical courses: rapid involuting course with long‐term remission and chronic course without remission. There was a tendency toward younger age of onset with elevated ASO titer in patients with rapid involuting course.
Immunoglobulin G‐dependent changes in basophil allergen threshold sensitivity during birch pollen immunotherapy
Authors: Lalek N. , Kosnik M. , Silar M. , Korosec P.
Published: May 2010

Background
The effects of pollen immunotherapy on effector cells of allergic inflammation, such as mast cells and basophils, are poorly understood.

Objective
For this reason, we conducted an open study on basophil allergen threshold sensitivity during birch pollen immunotherapy.

Methods
Basophil sensitivity was measured by CD63 flow cytometry in 14 patients with moderate–severe intermittent birch pollen rhinitis using four log allergen concentrations. In nine patients, we analysed the basophil sensitivity before and during treatment with subcutaneous birch immunotherapy (perennial scheme with allergoid). We also included eight birch‐allergic donor subjects for IgG inhibition experiments and eight control subjects.

Results
There was a decrease in basophil allergen threshold sensitivity after 2, 3, and 5 months of immunotherapy. This decrease was correlated with an improvement in patients' symptoms measured on a visual analogue scale. The serum obtained after immunotherapy induced a significant decrease in allergen threshold sensitivity in donor birch‐allergic basophils. This inhibition was not observed after IgG depletion from the serum.

Conclusions
In this study, we showed that birch immunotherapy‐induced IgG antibodies are associated with a reduction in basophil allergen threshold sensitivity. Further studies are needed to show whether the changes in basophil sensitivity are of clinical relevance in pollen immunotherapy.

Cite this as: N. Lalek, M. Kosnik, M. Silar and P. Korosec, Clinical & Experimental Allergy, 2010 (40) 1186–1193.
Nuclear fluorescence serum reactivity on monkey oesophagus: a new antibody for the follow-up of coeliac disease?
Authors: Picarelli A , Sabbatella L , Di Tola M , Silano M , Nicolussi A , D'Inzeo S , Coppa A
Published: May 2010

We have identified previously a nuclear fluorescence reactivity (NFR) pattern on monkey oesophagus sections exposed to coeliac disease (CD) patients' sera positive for anti-endomysium antibodies (EMA). The aim of the present work was to characterize the NFR, study the time–course of NFR-positive results in relation to gluten withdrawal and evaluate the potential role of NFR in the follow-up of CD. Twenty untreated, 87 treated CD patients and 15 healthy controls were recruited and followed for 12 months. Their sera were incubated on monkey oesophagus sections to evaluate the presence of NFR by indirect immunofluorescence analysis. Duodenal mucosa samples from treated CD patients were challenged with gliadin peptides, and thus the occurrence of NFR in culture supernatants was assessed. The NFR immunoglobulins (Igs) reactivity with the nuclear extract of a human intestinal cell line was investigated. Serum NFR was present in all untreated CD patients, persisted up to 151 ± 37 days from gluten withdrawal and reappeared in treated CD patients under dietary transgressions. Serum NFR was also detected in two healthy controls. In culture supernatants of coeliac intestinal mucosa challenged with gliadin peptides, NFR appeared before EMA. The Igs responsible for NFR were identified as belonging to the IgA2 subclass. The NFR resulted differently from EMA and anti-nuclear antibodies, but reacted with two nuclear antigens of 65 and 49 kDa. A new autoantibody, named NFR related to CD, was described. Furthermore, NFR detection might become a valuable tool in monitoring adherence to a gluten-free diet and identifying slight dietary transgressions.
Rituximab treatment in patients with active Graves' orbitopathy: effects on proinflammatory and humoral immune reactions
Authors: Vannucchi G , Campi I , Bonomi M , Covelli D , Dazzi D , Currò N , Simonetta S , Bonara P , Persani L , Guastella C , Wall J , Beck-Peccoz P , Salvi M
Published: May 2010

In active Graves' orbitopathy (GO), proinflammatory cytokines predominate. Circulating thyroid stimulating hormone (TSH)-receptor antibodies (TRAb) have been correlated with GO clinical activity and severity. In preliminary studies rituximab (RTX), an anti-CD 20 monoclonal antibody, has induced clinical improvement of active GO without a change in serum anti-thyroid antibodies. We have studied whether RTX in GO acts by affecting proinflammatory cytokines and thyroid and orbital-directed antibodies. Ten patients with GO were treated with RTX, administered twice intravenously (i.v.) (1000 mg) at days 1 and 15, and 20 with methylprednisolone, administered weekly i.v. (500 mg), for 16 weeks. Patients were studied before treatment, at B cell depletion and at 4, 8, 16, 20, 30 and 50 weeks. Peripheral lymphocytes, serum interleukin (sIL)-6, sIL-6r, chemokine (C-X-C motif) ligand 10 (CXCL10), TRAb and stimulating antibodies (TSAb) and autoantibodies against orbital calsequestrin, collagen XIII and flavoprotein subunit of succinate dehydrogenase (FP-SDH) were measured at baseline and after treatment. Serum IL-6 and sIL-6R concentrations did not change after RTX [P = not significant (n.s.)]. Serum CXCL10 increased after RTX at B cell depletion and at 30 weeks (P < 0·003). Serum TSAb did not change in relation to TRAb, nor did antibodies against orbital antigens (P = n.s.). In conclusion, this study shows that RTX in GO does not affect humoral reactions. The observed increase of serum CXCL10 concentrations at B cell depletion may result from cell lysis. We suggest that RTX may exert its effect in GO by inhibiting B cell antigen presentation.
Immunotherapy prospects for acute myeloid leukaemia
Authors: Barrett A J , Le Blanc K
Published: May 2010

While chemotherapy is successful at inducing remission of acute myeloid leukaemia (AML), the disease has a high probability of relapse. Strategies to prevent relapse involve consolidation chemotherapy, stem cell transplantation and immunotherapy. Evidence for immunosurveillance of AML and susceptibility of leukaemia cells to both T cell and natural killer (NK) cell attack and justifies the application of immune strategies to control residual AML persisting after remission induction. Immune therapy for AML includes allogeneic stem cell transplantation, adoptive transfer of allogeneic or autologous T cells or NK cells, vaccination with leukaemia cells, dendritic cells, cell lysates, peptides and DNA vaccines and treatment with cytokines, antibodies and immunomodulatory agents. Here we describe what is known about the immunological features of AML at presentation and in remission, the current status of immunotherapy and strategies combining treatment approaches with a view to achieving leukaemia cure.
Trail‐sharing among tropical ants: interspecific use of trail pheromones?
Authors: MENZEL FLORIAN , POKORNY TAMARA , BLÜTHGEN NICO , SCHMITT THOMAS
Published: May 2010

1. Trail‐sharing between different ant species is rare and restricted to a small number of species pairs. Its underlying mechanisms are largely unknown. For trail‐sharing to occur, two factors are required: (i) one or both species must recognise the other species or its pheromone trails and (ii) both species must tolerate each other to a certain extent to allow joint use of the trail. A species that follows another's trails can efficiently exploit the other's information on food sources contained in the pheromone trails. Hence, food competition and thus aggressive interactions between a species following another's trail and the species being followed, seem likely.

2. In the present study, we investigated interspecific trail following and interspecific aggression in trail sharing associations (i) among Polyrhachis ypsilon, Camponotus saundersi, and Dolichoderus cuspidatus, and (ii) among Camponotus rufifemur and Crematogaster modiglianii. We tested whether trail‐sharing species follow each other's pheromone trails, and whether the ants tolerated or attacked their trail‐sharing partners. In both associations, we confronted workers with pheromone trails of their associated species, and, for the former association, measured interspecific aggression among the trail‐sharing species.

3. In our assays, D. cuspidatus and C. rufifemur regularly followed heterospecific pheromone trails of P. ypsilon and C. modiglianii, respectively. However, only few workers of the remaining species followed heterospecific pheromone trails. Thus, shared trails of P. ypsilon and C. saundersi cannot be explained by interspecific trail‐following.

4. Interspecific aggression among P. ypsilon, C. saundersi, and D. cuspidatus was strongly asymmetric, C. saundersi being submissive to the other two. All three species differentiated between heterospecific workers from the same or another site, suggesting habituation to the respective trail‐sharing partners. We therefore hypothesise that differential tolerance by dominant ant species may be mediated by selective habituation towards submissive species and this way determines the assembly of trail‐sharing associations.