bluuebunny/crossref_metadata_2025 huggingface dataset:
Raman-active Fröhlich optical phonon mode in arsenic implanted ZnO
Authors: Ye J. D. , Tripathy S. , Ren Fang-Fang , Sun X. W. , Lo G. Q. , Teo K. L.
Published: January 2009

In this letter, using both off-resonant and resonant Raman spectroscopic techniques, the correlation of optical phonons and structural disorder in As+ implanted ZnO single crystals has been investigated. An additional broad peak shoulder at 550 cm−1 between the transverse optical and longitudinal optical (LO) phonons was clarified to be resonant Fröhlich optical phonon mode in the framework of effective dielectric function. Under resonance condition, an asymmetric broadening and softening of the LO phonon along with a blueshifted luminescent peak revealed the decreasing phonon coherent length and nanocrystallization with increasing fluence, respectively, in good agreement with the observations of transmission electron microscopy and atomic force microscopy.
Ferromagnetism in Ni-doped ZnO films: Extrinsic or intrinsic?
Authors: Snure Michael , Kumar Dhananjay , Tiwari Ashutosh
Published: January 2009

Here we report a detailed study aimed on understanding the origin of ferromagnetism in Ni-doped ZnO films. A pulsed laser deposition technique was used to deposit Ni-doped (5 at. %) ZnO films on sapphire (0001) substrates under different oxygen pressures ranging from 10−6 to 0.1 Torr. Films were characterized using numerous characterization techniques including x-ray diffraction, x-ray photospectroscopy, energy dispersive x-ray spectroscopy, optical absorption spectroscopy, and electrical transport, magnetotransport, and magnetization measurements. A detailed structure-property correlation and analysis of our results revealed that the ferromagnetism in ZnO:Ni films is not an inherent property of the material but results due to a strong tendency of Ni to precipitate out in the ZnO matrix.
Surface effects on the elastic modulus of nanoporous materials
Authors: Feng Xi-Qiao , Xia Re , Li Xide , Li Bo
Published: January 2009

The mechanical properties of a nanoporous material depend not only on its porosity but also on its characteristic sizes of microstructure, e.g., the average sizes of ligaments. Classical continuum mechanics models cannot interpret this type of size dependence. We here present a unit-cell micromechanics model to predict the effective Young’s modulus of open-cell nanoporous materials. The theory of surface elasticity is adopted to incorporate the effects of surface energy and residual surface stress on the effective elastic property of nanoporous materials. This model can reasonably elucidate the relevant experimental results.
Optical and electrical characteristics of Ag-doped perylene diimide derivative
Authors: Chiu Tien-Lung , Xu Wei-Feng , Lin Chi-Feng , Lee Jiun-Haw , Chao Chun-Chieh , Leung Man-Kit
Published: January 2009

In this paper, a highly conductive and strongly absorptive organic thin film by doping Ag into N,N′-bis (2,6-di-isopropylphenyl)-1,7-bis (4-methoxy-phenyl) perylene-3,4,9,10-tetracarboxydiimide (MPPDI) was demonstrated. Strong absorption resulted from the broadband absorption of MPPDI at visible range and plasmon-enhanced absorption around 420 nm of Ag nanoparticles. Ag dopants in MPPDI acted as quenchers, which resulted in a dramatic decrease in photoluminescence intensity of MPPDI. Besides, J-V characteristics of Ag:MPPDI thin film changed from trapped-charge-limited current to Ohmic conduction with increasing Ag concentrations. Conductivity of 1.15×10−6 Ω cm was achieved when MPPDI/Ag=5:1. This organic thin film has potential applications for low-reflectance organic light-emitting diode and organic photovoltaic device.
Modeling of negatively charged states at the Ge surface and interfaces
Authors: Tsipas P. , Dimoulas A.
Published: January 2009

Modeling based on surface charge neutrality predicts that the Ge surface tends to be p-type, irrespective of the bulk conductivity. This is a consequence of the fact that the Ge band gap is small and the charge neutrality level lies low in the gap very close to the valence band, probably determined by low-lying unpassivated surface dangling bond acceptors or other defects. According to the model, the acceptor defects build negative charge, inverting the surface of n-type Ge at no gate bias for low doping concentration (<1016 cm−3) and moderate or high interface state densities (>5×1011 eV−1 cm−2). This is predicted to cause undesired positive threshold voltage shift in the range of 0.2–0.4 V in Ge p-channel field effect transistors. The model also predicts that inversion in n-channel field effect transistors is inhibited, which could be related to the observed poor performance of these devices.
Efficient microfluidic particle separation arrays
Authors: Inglis David W.
Published: January 2009

Microfluidic particle separation arrays are capable of passive sorting of microparticles or cells by size while avoiding blockage. Despite the usefulness of boundaries for concentration and parallel integration of arrays, separation efficiency is severely degraded in the areas adjacent to the boundaries due to the aberrant fluid flow found there. This letter shows how to eliminate this problem by modifying the boundary interface. At each row the boundary is moved by a specific amount to ensure a linear change in flux from row to row, which leads to uniform flow patterns and improved separation characteristics throughout the array.
Allelic recombination between distinct genomic locations generates copy number diversity in human β-defensins
Authors: Bakar Suhaili Abu , Hollox Edward J. , Armour John A. L.
Published: January 2009

β-Defensins are small secreted antimicrobial and signaling peptides involved in the innate immune response of vertebrates. In humans, a cluster of at least 7 of these genes shows extensive copy number variation, with a diploid copy number commonly ranging between 2 and 7. Using a genetic mapping approach, we show that this cluster is at not 1 but 2 distinct genomic loci ≈5 Mb apart on chromosome band 8p23.1, contradicting the most recent genome assembly. We also demonstrate that the predominant mechanism of change in β-defensin copy number is simple allelic recombination occurring in the interval between the 2 distinct genomic loci for these genes. In 416 meiotic transmissions, we observe 3 events creating a haplotype copy number not found in the parent, equivalent to a germ-line rate of copy number change of ≈0.7% per gamete. This places it among the fastest-changing copy number variants currently known.
Localized and efficient curli nucleation requires the chaperone-like amyloid assembly protein CsgF
Authors: Nenninger Ashley A. , Robinson Lloyd S. , Hultgren Scott J.
Published: January 2009

Elucidation of the early events in amyloidogenesis is key to understanding the pathology of, and developing therapies for, amyloid diseases. Critical informants about these early events are amyloid assembly proteins that facilitate the transition from monomer to amyloid fiber. Curli are a functional amyloid whose in vivo polymerization requires a dedicated nucleator protein, CsgB, and an assembly protein, CsgF. Here we demonstrate that without CsgF, curli subunits are released from the cell into the media and are inefficiently polymerized, resulting in fewer and mislocalized curli fibers. CsgF is secreted to the cell surface, where it mediates the cell-association and protease-resistance of the CsgB nucleator, suggesting that CsgF is required for specific localization and/or chaperoning of CsgB for full nucleator activity. CsgF is thus critical to achieve localized and efficient nucleation of fiber subunits into functional, cell-associated amyloid.
Observations of counter-current toroidal rotation in Alcator C-Mod LHCD plasmas
Authors: Rice J.E. , Ince-Cushman A.C. , Bonoli P.T. , Greenwald M.J. , Hughes J.W. , Parker R.R. , Reinke M.L. , Wallace G.M. , Fiore C.L. , Granetz R.S. , Hubbard A.E. , Irby J.H. , Marmar E.S. , Shiraiwa S. , Wolfe S.M. , Wukitch S.J. , Bitter M. , Hill K. , Wilson J.R.
Published: January 2009

Following the application of lower hybrid current drive (LHCD) power, the core toroidal rotation in Alcator C-Mod L- and H-mode plasmas is found to increment in the counter-current direction, in conjunction with a decrease in the plasma internal inductance, l
i. Along with the drops in l
i and the core rotation velocity, there is peaking of the electron and impurity density profiles, as well as of the ion and electron temperature profiles. The mechanism generating the counter-current rotation is unknown, but it is consistent in sign with an inward shift of energetic electron orbits, giving rise to a negative core radial electric field. The peaking in the density, toroidal rotation (in the counter-current direction) and temperature profiles occurs over a time scale similar to the current relaxation time but slow compared with the energy and momentum confinement times. Most of these discharges exhibit sawtooth oscillations throughout, with the inversion radius shifting inward during the LHCD and profile evolution. The magnitudes of the changes in the internal inductance and the central rotation velocity are strongly correlated and found to increase with increasing LHCD power and decreasing electron density. The maximum effect is obtained with a waveguide phasing of 60° (a launched parallel index of refraction n
‖ ∼ 1.5), with a significantly smaller magnitude at 120° (n
‖ ∼ 3.1), and with no effect for negative or heating (180°) phasing. Regardless of the plasma parameters and launched n
‖ of the waves, there is a strong correlation between the rotation velocity and l
i changes, possibly providing a clue for the underlying mechanism.
Prequips—an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data
Authors: Gehlenborg Nils , Yan Wei , Lee Inyoul Y. , Yoo Hyuntae , Nieselt Kay , Hwang Daehee , Aebersold Ruedi , Hood Leroy
Published: January 2009

Summary: We describe an integrative software platform, Prequips, for comparative proteomics-based systems biology analysis that: (i) integrates all information generated from mass spectrometry (MS)-based proteomics as well as from basic proteomics data analysis tools, (ii) visualizes such information for various proteomic analyses via graphical interfaces and (iii) links peptide and protein abundances to external tools often used in systems biology studies.

Availability:  http://prequips.sourceforge.net

Contact:  dhhwang@postech.ac.kr
Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools
Authors: Qi Qihao , Zhao Yingdong , Li MingChung , Simon Richard
Published: January 2009

Summary: Non-negative matrix factorization (NMF) is an increasingly used algorithm for the analysis of complex high-dimensional data. BRB-ArrayTools is a widely used software system for the analysis of gene expression data with almost 9000 registered users in over 65 countries. We have developed a NMF analysis plug-in in BRB-ArrayTools for unsupervised sample clustering of microarray gene expression data. Our analysis tool also incorporates an algorithm for Semi-NMF which can handle both positive and negative elements for log-ratio data. Output includes a heat map of sample clusters and differentially expressed genes with extensive biological annotation. For comparison, output also includes the results of K-means clustering.

Availability: The NMF analysis plug-in is freely available in BRB-ArrayTools for non-commercial users. BRB-ArrayTools can be downloaded at http://linus.nci.nih.gov/BRB-ArrayTools.html. The algorithms used for NMF and Semi-NMF are available at ftp://linus.nci.nih.gov/pub/NMF.

Contact: rsimon@mail.nih.gov
Human microRNAs co-silence in well-separated groups and have different predicted essentialities
Authors: Boross Gábor , Orosz Katalin , Farkas Illés J.
Published: January 2009

Background: Short regulating RNAs guide many cellular processes. Compared with transcription factor proteins they appear to provide more specialized control and their deletions are less frequently lethal.

Results: We find large differences between computationally predicted lists of human microRNA (miRNA)–target pairs. Instead of integrating these lists we use the two most accurate of them. Next, we construct the co-regulation network of human miRNAs as nodes by computing the correlation (link weight) between the gene silencing scores of individual miRNAs. In this network, we locate groups of tightly co-regulating nodes (modules). Despite explicitly allowing overlaps the co-regulation modules of miRNAs are well separated. We use the modules and miRNA co-expression data to define and compute miRNA essentiality. Instead of focusing on particular biological functions we identify a miRNA as essential, if it has a low co-expression with the miRNAs in its module. This may be thought of as having many workers performing the same tasks together in one place (non-essential miRNAs) as opposed to a single worker performing those tasks alone (essential miRNA).

Conclusions: On the system level, we quantitatively confirm previous findings about the specialized control provided by miRNAs. For knock-out tests we list the groups of our predicted most and least essential miRNAs. In addition, we provide possible explanations for (i) the low number of individually essential miRNAs in Caenorhabdtits elegans and (ii) the high number of ubiquitous miRNAs influencing cell and tissue-specific miRNA expression patterns in mouse and human.

Contact:  fij@elte.hu

Supplementary information:  Supplementary data are available at Bioinformatics online.
A Chinese Herbal Decoction, Danggui Buxue Tang, Stimulates Proliferation, Differentiation and Gene Expression of Cultured Osteosarcoma Cells: Genomic Approach to Reveal Specific Gene Activation
Authors: Choi Roy C. Y. , Gao Qiu T. , Cheung Anna W. H. , Zhu Judy T. T. , Lau Faye T. C. , Li Jun , Li Winnie Z. M. , Chu Glanice K. Y. , Duan Ran , Cheung Jerry K. H. , Ding An W. , Zhao Kui J. , Dong Tina T. X. , Tsim Karl W. K.
Published: January 2009

Danggui Buxue Tang (DBT), a Chinese herbal decoction used to treat ailments in women, contains Radix Astragali (Huangqi; RA) and Radix Angelicae Sinensis (Danggui; RAS). When DBT was applied onto cultured MG‐63 cells, an increase of cell proliferation and differentiation of MG‐63 cell were revealed: both of these effects were significantly higher in DBT than RA or RAS extract. To search for the biological markers that are specifically regulated by DBT, DNA microarray was used to reveal the gene expression profiling of DBT in MG‐63 cells as compared to that of RA‐ or RAS‐treated cells. Amongst 883 DBT‐regulated genes, 403 of them are specifically regulated by DBT treatment, including CCL‐2, CCL‐7, CCL‐8, and galectin‐9. The signaling cascade of this DBT‐regulated gene expression was also elucidated in cultured MG‐63 cells. The current results reveal the potential usage of this herbal decoction in treating osteoporosis and suggest the uniqueness of Chinese herbal decoction that requires a well‐defined formulation. The DBT‐regulated genes in the culture could serve as biological responsive markers for quality assurance of the herbal preparation.
Screening Antitumor Compounds Psoralen and Isopsoralen from Psoralea corylifolia L. Seeds
Authors: Wang Yi , Hong Chengtao , Zhou Chenguang , Xu Dongmei , Qu Hai-bin
Published: January 2009

Psoralea corylifolia L. (Fabaceae) is a widely used medical plant in China. This study was designed to screen and identify bioactive compounds with anticancer activity from the seeds of Psoralea corylifolia L. One volatile fraction (fraction I) and three other fractions (fraction II, III, IV) from methanol extraction of P. corylifolia L. were obtained. Bioactivities of these fractions were evaluated by the cytotoxicity on KB, KBv200, K562, K562/ADM cancer cells with MTT assay. Major components in the active fraction were identified by HPLC/MSn. Fraction IV significantly inhibits the growth of cancer cells in a dose‐dependent manner. The IC50 values were 21.6, 24.4, 10.0 and 26.9, respectively. Psoralen and isopsoralen, isolated from fraction IV, were subject to bioactive assay and presented a dose‐dependent anticancer activity in four cancer cell lines (KB, KBv200, K562 and K562/ADM). The IC50 values of psoralen were 88.1, 86.6, 24.4 and 62.6, which of isopsoralen were 61.9, 49.4, 49.6 and 72.0, respectively. Apoptosis of tumor cell significantly increased after treated with psoralen and isopsoralen. Induction of apoptotic activity was confirmed by flow cytometry after staining with Annexin V/PI. These results suggested psoralen and isopsoralen contribute to anticancer effect of P. corylifolia L.
The TIR Domain of TIR-NB-LRR Resistance Proteins Is a Signaling Domain Involved in Cell Death Induction
Authors: Swiderski Michal R. , Birker Doris , Jones Jonathan D. G.
Published: January 2009

In plants, the TIR (toll interleukin 1 receptor) domain is found almost exclusively in nucleotide-binding (NB) leucine-rich repeat resistance proteins and their truncated homologs, and has been proposed to play a signaling role during resistance responses mediated by TIR containing R proteins. Transient expression in Nicotiana benthamiana leaves of “TIR + 80”, the RPS4 truncation without the NB-ARC domain, leads to EDS1-, SGT1-, and HSP90-dependent cell death. Transgenic Arabidopsis plants expressing the RPS4 TIR+80 from either dexamethasone or estradiol-inducible promoters display inducer-dependent cell death. Cell death is also elicited by transient expression of similarly truncated constructs from two other R proteins, RPP1A and At4g19530, but is not elicited by similar constructs representing RPP2A and RPP2B proteins. Site-directed mutagenesis of the RPS4 TIR domain identified many loss-of-function mutations but also revealed several gain-of function substitutions. Lack of cell death induction by the E160A substitution suggests that amino acids outside of the TIR domain contribute to cell death signaling in addition to the TIR domain itself. This is consistent with previous observations that the TIR domain itself is insufficient to induce cell death upon transient expression.
Activation of the Salicylic Acid Signaling Pathway Enhances Clover yellow vein virus Virulence in Susceptible Pea Cultivars
Authors: Atsumi Go , Kagaya Uiko , Kitazawa Hiroaki , Nakahara Kenji Suto , Uyeda Ichiro
Published: January 2009

The wild-type strain (Cl-WT) of Clover yellow vein virus (ClYVV) systemically induces cell death in pea cv. Plant introduction (PI) 118501 but not in PI 226564. A single incompletely dominant gene, Cyn1, controls systemic cell death in PI 118501. Here, we show that activation of the salicylic acid (SA) signaling pathway enhances ClYVV virulence in susceptible pea cultivars. The kinetics of virus accumulation was not significantly different between PI 118501 (Cyn1) and PI 226564 (cyn1); however, the SA-responsive chitinase gene (SA-CHI) and the hypersensitive response (HR)-related gene homologous to tobacco HSR203J were induced only in PI 118501 (Cyn1). Two mutant viruses with mutations in P1/HCPro, which is an RNA-silencing suppressor, reduced the ability to induce cell death and SA-CHI expression. The application of SA and of its analog benzo (1,2,3) thiadiazole-7-carbothioic acid S-methyl ester (BTH) partially complemented the reduced virulence of mutant viruses. These results suggest that high activation of the SA signaling pathway is required for ClYVV virulence. Interestingly, BTH could enhance Cl-WT symptoms in PI 226564 (cyn1). However, it could not enhance symptoms induced by White clover mosaic virus and Bean yellow mosaic virus. Our report suggests that the SA signaling pathway has opposing functions in compatible interactions, depending on the virus–host combination.
First Report of Bamboo Rust Caused by Kweilingia divina on Bambusa domestica in Los Angeles County, California
Authors: Blomquist C. L. , McKemy J. M. , Aime M. C. , Orsburn R. W. , Kinnee S. A.
Published: January 2009

Elongate, interveinal, hypophyllous lesions were observed on bamboo plants (Bambusa domestica) during an inspection of a plant shipment in November of 2006 in Los Angeles County, CA. Disease incidence was 100%. Minute uredinia were spaced at regular intervals within each lesion. Urediniospores were pale tan, echinulate, and 18 to 29 × 16 to 23 μm with 1- to 1.5-μm walls. The urediniospores were surrounded and partially covered by incurved pale-to-brownish yellow paraphyses 34 to 45 × 12 μm with walls that were primarily thickened apically and dorsally to 5 μm. Several telia were observed forming inside old uredinia. Telia were brownish black, forming a flabellar head of teliospores fused laterally and in chains of three to six cells. Teliospores were chestnut brown, cuboidal to oblong, and measured 10 to 12.5 × 12.5 to 25 μm. DNA sequence of the 28S large subunit nuclear ribosomal DNA was obtained using previously published methods (1). The sequence deposited in GenBank as Accession No. EF192212 matched sequence No. DQ354554 (1), Kweilingia divina from Costa Rica (1), with 100% identity. On the basis of morphological characteristics (2) and sequence information, the rust was identified as K. divina (Syd.) Buriticá (= Dasturella divina (Syd.) Mundk. & Khesw.), causal agent of bamboo rust. Bamboo rust is widespread in parts of Asia but has also been found in Africa, Colombia, Brazil, Central America (3), and Australia (4). The shipment was traced to a foliage plant producer in Hawaii where the disease was subsequently found in the environment on the four major Hawaiian Islands of Oahu, Hawaii, Kauai, and Maui. All 10 bamboo plants received by the nursery were located and destroyed. To the best of our knowledge, this is the first report of bamboo rust occurring in California.

References: (1) M. C. Aime. Mycoscience 47:112, 2006. (2) G. B. Cummins. Page 43 in: The Rust Fungi of Cereals, Grasses and Bamboos. Springer-Verlag, New York, 1971. (3) D. F. Farr et al. Fungal Databases, Systematic Mycology and Microbiology Laboratory. Online publication. ARS, USDA, year. (4) G. I. Johnson. Australas. Plant Pathol. 14:54, 1985.
A bizarre Cretaceous theropod dinosaur from Patagonia and the evolution of Gondwanan dromaeosaurids
Authors: Novas Fernando E , Pol Diego , Canale Juan I , Porfiri Juan D , Calvo Jorge O
Published: January 2009

Fossils of a predatory dinosaur provide novel information about the evolution of unenlagiines, a poorly known group of dromaeosaurid theropods from Gondwana. The new dinosaur is the largest dromaeosaurid yet discovered in the Southern Hemisphere and depicts bizarre cranial and postcranial features. Its long and low snout bears numerous, small-sized conical teeth, a condition resembling spinosaurid theropods. Its short forearms depart from the characteristically long-armed condition of all dromaeosaurids and their close avian relatives. The new discovery amplifies the range of morphological disparity among unenlagiines, demonstrating that by the end of the Cretaceous this clade included large, short-armed forms alongside crow-sized, long-armed, possibly flying representatives. The new dinosaur is the youngest record of dromaeosaurids from Gondwana and represents a previously unrecognized lineage of large predators in Late Cretaceous dinosaur faunas mainly dominated by abelisaurid theropods.
Phosphorylation of Swi6/HP1 regulates transcriptional gene silencing at heterochromatin
Authors: Shimada Atsushi , Dohke Kohei , Sadaie Mahito , Shinmyozu Kaori , Nakayama Jun-Ichi , Urano Takeshi , Murakami Yota
Published: January 2009

Heterochromatin protein 1 (HP1) recruits various effectors to heterochromatin for multiple functions, but its regulation is unclear. In fission yeast, a HP1 homolog Swi6 recruits SHREC, Epe1, and cohesin, which are involved in transcriptional gene silencing (TGS), transcriptional activation, and sister chromatid cohesion, respectively. We found that casein kinase II (CK2) phosphorylated Swi6. Loss of CK2-dependent Swi6 phosphorylation alleviated heterochromatic TGS without affecting heterochromatin structure. This was due to the inhibited recruitment of SHREC to heterochromatin, accompanied by an increase in Epe1. Interestingly, loss of phosphorylation did not affect cohesion. These results indicate that CK2-dependent Swi6 phosphorylation specifically controls TGS in heterochromatin.
Systemic regulation of starvation response in Caenorhabditis elegans
Authors: Kang Chanhee , Avery Leon
Published: January 2009

When the supply of environmental nutrients is limited, multicellular animals can make both physiological and behavioral changes so as to cope with nutrient starvation. Although physiological and behavioral effects of starvation are well known, the mechanisms by which animals sense starvation systemically remain elusive. Furthermore, what constituent of food is sensed and how it modulates starvation response is still poorly understood. In this study, we use a starvation-hypersensitive mutant to identify molecules and mechanisms that modulate starvation signaling. We found that specific amino acids could suppress the starvation-induced death of gpb-2 mutants, and that MGL-1 and MGL-2, Caenorhabditis elegans homologs of metabotropic glutamate receptors, were involved. MGL-1 and MGL-2 acted in AIY and AIB neurons, respectively. Treatment with leucine suppressed starvation-induced stress resistance and life span extension in wild-type worms, and mutation of mgl-1 and mgl-2 abolished these effects of leucine. Taken together, our results suggest that metabotropic glutamate receptor homologs in AIY and AIB neuron may modulate a systemic starvation response, and that C. elegans senses specific amino acids as an anti-hunger signal.
E2f3b plays an essential role in myogenic differentiation through isoform-specific gene regulation
Authors: Asp Patrik , Acosta-Alvear Diego , Tsikitis Mary , van Oevelen Chris , Dynlacht Brian David
Published: January 2009

Current models posit that E2F transcription factors can be divided into members that either activate or repress transcription, in part through collaboration with the retinoblastoma (pRb) tumor suppressor family. The E2f3 locus encodes E2f3a and E2f3b proteins, and available data suggest that they regulate cell cycle-dependent gene expression through opposing transcriptional activating and repressing activities in growing and quiescent cells, respectively. However, the role, if any, of E2F proteins, and in particular E2f3, in myogenic differentiation is not well understood. Here, we dissect the contributions of E2f3 isoforms and other activating and repressing E2Fs to cell cycle exit and differentiation by performing genome-wide identification of isoform-specific targets. We show that E2f3a and E2f3b target genes are involved in cell growth, lipid metabolism, and differentiation in an isoform-specific manner. Remarkably, using gene silencing, we show that E2f3b, but not E2f3a or other E2F family members, is required for myogenic differentiation, and that this requirement for E2f3b does not depend on pRb. Our functional studies indicate that E2f3b specifically attenuates expression of genes required to promote differentiation. These data suggest how diverse E2F isoforms encoded by a single locus can play opposing roles in cell cycle exit and differentiation.
Yeast Mph1 helicase dissociates Rad51-made D-loops: implications for crossover control in mitotic recombination
Authors: Prakash Rohit , Satory Dominik , Dray Eloïse , Papusha Almas , Scheller Jürgen , Kramer Wilfried , Krejci Lumir , Klein Hannah , Haber James E. , Sung Patrick , Ira Grzegorz
Published: January 2009

Eukaryotes possess mechanisms to limit crossing over during homologous recombination, thus avoiding possible chromosomal rearrangements. We show here that budding yeast Mph1, an ortholog of human FancM helicase, utilizes its helicase activity to suppress spontaneous unequal sister chromatid exchanges and DNA double-strand break-induced chromosome crossovers. Since the efficiency and kinetics of break repair are unaffected, Mph1 appears to channel repair intermediates into a noncrossover pathway. Importantly, Mph1 works independently of two other helicases—Srs2 and Sgs1—that also attenuate crossing over. By chromatin immunoprecipitation, we find targeting of Mph1 to double-strand breaks in cells. Purified Mph1 binds D-loop structures and is particularly adept at unwinding these structures. Importantly, Mph1, but not a helicase-defective variant, dissociates Rad51-made D-loops. Overall, the results from our analyses suggest a new role of Mph1 in promoting the noncrossover repair of DNA double-strand breaks.
GLI1 is regulated through Smoothened-independent mechanisms in neoplastic pancreatic ducts and mediates PDAC cell survival and transformation
Authors: Nolan-Stevaux Olivier , Lau Janet , Truitt Morgan L. , Chu Gerald C. , Hebrok Matthias , Fernández-Zapico Martin E. , Hanahan Douglas
Published: January 2009

Pancreatic ductal adenocarcinoma (PDAC) is characterized by the deregulation of the hedgehog signaling pathway. The Sonic Hedgehog ligand (Shh), absent in the normal pancreas, is highly expressed in pancreatic tumors and is sufficient to induce neoplastic precursor lesions in mouse models. We investigated the mechanism of Shh signaling in PDAC carcinogenesis by genetically ablating the canonical bottleneck of hedgehog signaling, the transmembrane protein Smoothened (Smo), in the pancreatic epithelium of PDAC-susceptible mice. We report that multistage development of PDAC tumors is not affected by the deletion of Smo in the pancreas, demonstrating that autocrine Shh–Ptch–Smo signaling is not required in pancreatic ductal cells for PDAC progression. However, the expression of Gli target genes is maintained in Smo-negative ducts, implicating alternative means of regulating Gli transcription in the neoplastic ductal epithelium. In PDAC tumor cells, we find that Gli transcription is decoupled from upstream Shh–Ptch–Smo signaling and is regulated by TGF-β and KRAS, and we show that Gli1 is required both for survival and for the KRAS-mediated transformed phenotype of cultured PDAC cancer cells.
PRMT1-mediated arginine methylation of PIAS1 regulates STAT1 signaling
Authors: Weber Susanne , Maaß Florian , Schuemann Michael , Krause Eberhard , Suske Guntram , Bauer Uta-Maria
Published: January 2009

To elucidate the function of the transcriptional coregulator PRMT1 (protein arginine methyltranferase 1) in interferon (IFN) signaling, we investigated the expression of STAT1 (signal transducer and activator of transcription) target genes in PRMT1-depleted cells. We show here that PRMT1 represses a subset of IFNγ-inducible STAT1 target genes in a methyltransferase-dependent manner. These genes are also regulated by the STAT1 inhibitor PIAS1 (protein inhibitor of activated STAT1). PIAS1 is arginine methylated by PRMT1 in vitro as well as in vivo upon IFN treatment. Mutational and mass spectrometric analysis of PIAS1 identifies Arg 303 as the single methylation site. Using both methylation-deficient and methylation-mimicking mutants, we find that arginine methylation of PIAS1 is essential for the repressive function of PRMT1 in IFN-dependent transcription and for the recruitment of PIAS1 to STAT1 target gene promoters in the late phase of the IFN response. Methylation-dependent promoter recruitment of PIAS1 results in the release of STAT1 and coincides with the decline of STAT1-activated transcription. Accordingly, knockdown of PRMT1 or PIAS1 enhances the anti-proliferative effect of IFNγ. Our findings identify PRMT1 as a novel and crucial negative regulator of STAT1 activation that controls PIAS1-mediated repression by arginine methylation.
Second messenger-mediated spatiotemporal control of protein degradation regulates bacterial cell cycle progression
Authors: Duerig Anna , Abel Sören , Folcher Marc , Nicollier Micael , Schwede Torsten , Amiot Nicolas , Giese Bernd , Jenal Urs
Published: January 2009

Second messengers control a wide range of important cellular functions in eukaryotes and prokaryotes. Here we show that cyclic di-GMP, a global bacterial second messenger, promotes cell cycle progression in Caulobacter crescentus by mediating the specific degradation of the replication initiation inhibitor CtrA. During the G1-to-S-phase transition, both CtrA and its cognate protease ClpXP dynamically localize to the old cell pole, where CtrA is rapidly degraded. Sequestration of CtrA to the cell pole depends on PopA, a newly identified cyclic di-GMP effector protein. PopA itself localizes to the cell pole and directs CtrA to this subcellular site via the direct interaction with a mediator protein, RcdA. We present evidence that c-di-GMP regulates CtrA degradation during the cell cycle by controlling the dynamic sequestration of the PopA recruitment factor to the cell pole. Furthermore, we show that cell cycle timing of CtrA degradation relies on converging pathways responsible for substrate and protease localization to the old cell pole. This is the first report that links cyclic di-GMP to protein dynamics and cell cycle control in bacteria.
Drosophila PTB promotes formation of high-order RNP particles and represses oskar translation
Authors: Besse Florence , López de Quinto Sonia , Marchand Virginie , Trucco Alvar , Ephrussi Anne
Published: January 2009

Local translation of asymmetrically enriched mRNAs is a powerful mechanism for functional polarization of the cell. In Drosophila, exclusive accumulation of Oskar protein at the posterior pole of the oocyte is essential for development of the future embryo. This is achieved by the formation of a dynamic oskar ribonucleoprotein (RNP) complex regulating the transport of oskar mRNA, its translational repression while unlocalized, and its translational activation upon arrival at the posterior pole. We identified the nucleo–cytoplasmic shuttling protein PTB (polypyrimidine tract-binding protein)/hnRNP I as a new factor associating with the oskar RNP in vivo. While PTB function is largely dispensable for oskar mRNA transport, it is necessary for translational repression of the localizing mRNA. Unexpectedly, a cytoplasmic form of PTB can associate with oskar mRNA and repress its translation, suggesting that nuclear recruitment of PTB to oskar complexes is not required for its regulatory function. Furthermore, PTB binds directly to multiple sites along the oskar 3′ untranslated region and mediates assembly of high-order complexes containing multiple oskar RNA molecules in vivo. Thus, PTB is a key structural component of oskar RNP complexes that dually controls formation of high-order RNP particles and translational silencing.
Examination of whewellite kidney stones by scanning electron microscopy and powder neutron diffraction techniques
Authors: Daudon Michel , Bazin Dominique , André Gilles , Jungers Paul , Cousson Alain , Chevallier Pierre , Véron Emmanuel , Matzen Guy
Published: January 2009

Kidney stones made of whewellite,i.e.calcium oxalate monohydrate, exhibit various morphological aspects. The crystalline structure of whewellite at the atomic scale was revisited through a single-crystal neutron study at room temperature using a four-circle automated diffractometer. The possible relationships between the various morphological types of whewellite stones and their structural characteristics were examined at the mesoscopic scale by the use of scanning electron microscopy and at the nanometric scale by powder neutron diffraction. All types of whewellite stones displayed a similar structure at the nanometric scale. However, significant differences were found at the mesoscopic scale. In particular, the crystallites in kidney stones resulting from a genetic hyperoxaluria exhibited a peculiar structure. There was a close relationship between stone morphology and crystallite organization at the mesoscopic level and the effectiveness of extracorporeal shockwave lithotripsy.
The RATIO method for time-resolved Laue crystallography
Authors: Coppens Philip , Pitak Mateusz , Gembicky Milan , Messerschmidt Marc , Scheins Stephan , Benedict Jason , Adachi Shin-ichi , Sato Tokushi , Nozawa Shunsuke , Ichiyanagi Kohei , Chollet Matthieu , Koshihara Shin-ya
Published: January 2009

A RATIO method for analysis of intensity changes in time-resolved pump–probe Laue diffraction experiments is described. The method eliminates the need for scaling the data with a wavelength curve representing the spectral distribution of the source and removes the effect of possible anisotropic absorption. It does not require relative scaling of series of frames and removes errors due to all but very short term fluctuations in the synchrotron beam.
Performance of the micro-PIC gaseous area detector in small-angle X-ray scattering experiments
Authors: Hattori Kaori , Tsuchiya Ken'ichi , Ito Kazuki , Okada Yoko , Fujii Kotaro , Kubo Hidetoshi , Miuchi Kentaro , Takata Masaki , Tanimori Toru , Uekusa Hidehiro
Published: January 2009

The application of a two-dimensional photon-counting detector based on a micro-pixel gas chamber (µ-PIC) to high-resolution small-angle X-ray scattering (SAXS), and its performance, are reported. The µ-PIC is a micro-pattern gaseous detector fabricated by printed circuit board technology. This article describes the performance of the µ-PIC in SAXS experiments at SPring-8. A dynamic range of >105 was obtained for X-ray scattering from a polystyrene sphere solution. A maximum counting rate of up to 5 MHz was observed with good linearity and without saturation. For a diffraction pattern of collagen, weak peaks were observed in the high-angle region in one accumulation of photons.
Dielectric properties of (NH4)2SO4 crystals in the range of electronic excitations
Authors: Andriyevsky B. , Cobet C. , Patryn A. , Esser N.
Published: January 2009

Spectra of the real and imaginary parts of the pseudo-dielectric permittivity, 〈∊1〉(E) and 〈∊2〉(E), of ferroelectric ammonium sulfate crystals, (NH4)2SO4, have been measured in the range of electronic excitations 4.0 to 9.5 eV by ellipsometry using synchrotron radiation. Temperature dependences of the corresponding susceptibilities, 〈χ1〉(T) and 〈χ2〉(T), obtained for the photon energy E = 8.5 eV, related to excitations of oxygen p-electrons, reveal sharp peak-like temperature changes near the Curie point T
C = 223 K. The large temperature-dependent increase of the imaginary part of the susceptibility χ2(T), together with a simultaneous decrease of the real part of the susceptibility χ1(T), take place at the phase transition. These anomalies have been ascribed mainly to the SO4 group of the crystal structure.
Questioning Research with Children: Discrepancy between Theory and Practice?
Authors: Uprichard Emma
Published: January 2009

This paper argues that current child and childhood research is problematical in as much as there is a discrepancy between theory and research practice. Although in theory, children are conceptualised as active agents in the social world, the type of research that children are typically involved in implies that children are competent, knowledgeable and affective only in terms of their own lives, their own spaces, their own childhoods. The implications of this discrepancy are discussed. The paper concludes that although research that contributes to a greater understanding of childhood experiences is important, it is equally important to involve children in research that goes beyond ‘childhood’.
What’s Recreational about ‘Recreational Rioting’? Children on the Streets in Belfast
Authors: Leonard Madeleine
Published: January 2009

The purpose of this paper was to explore teenagers’ perception of the concept of ‘recreational rioting’. It draws on focus group discussions with 80 Catholic and Protestant teenagers who live in one of the most contested interface areas in Northern Ireland, many of whom have experience of rioting. The majority of children who took part in the research were highly critical of the connotations associated with ‘recreational rioting’ and their experiences of rioting calls into question the ‘recreational’ aspects of the practice. While many children were motivated to become involved in rioting because of ‘something to do’, their participation was imbued with political undertones.
Stress Development Due to Capillary Condensation in Powder Compacts: A Two‐Dimensional Model Study
Authors: Lampenscherf Stefan , Pompe Wolfgang , Wilkinson David S.
Published: January 2009

A model experiment is presented to investigate the relationship between the humidity‐dependent liquid distribution and the macroscopic stress in a partially wet powder compact. Therefore, films of monosized spherical particles were cast on silicon substrates. Using environmental SEM the geometry of the liquid necks trapped between particles was imaged as a function of relative humidity. Simultaneously the macroscopic stress in the substrate adhered particle film was measured by capacitive deflection measurement. The experimentally found humidity dependence of the liquid neck size and the macroscopic film stress are compared with model predictions. The circle–circle approximation is used to predict the size of the liquid necks between touching particles as a function of the capillary pressure. Using the modified Kelvin relation between capillary pressure and relative humidity, we consider the effect of an additional solute which may be present in the capillary liquid. The results of the stress measurement are compared with the model predictions for a film of touching particles in hexagonal symmetry. The contribution of the capillary interaction to the adhesion force between neighboring particles is calculated using the integrated Laplace equation. The resulting film stress can be approximated relating this capillary force to an effective cross section per particle. The experimentally found humidity dependence of the liquid neck size is in good agreement with the model predictions for finite solute concentration. The film stress corresponds to the model predictions only for large relative humidities and shows an unexpected increase at small values. As is shown with an atomic force microscope, the real structure of the particle–particle contact area changes during the wet/dry cycle. A solution/reprecipitation process causes surface heterogeneities and solid bridging between the particles. It is claimed that the existence of a finite contact zone between the particles gives rise to the unexpected increase of the stress at small relative humidities.
Fabrication and Ultraviolet Absorption of Sol–Gel‐Derived Germanium Oxide Glass Thin Films
Authors: Jang Jae Hyeok , Koo Junmo , Bae Byeong‐Soo
Published: January 2009

Germanium oxide glass thin films were prepared by the sol–gel method and annealed under reduced atmosphere to create more oxygen‐deficient defects. The densification and crystallization were examined depending on sintering and annealing conditions. Thus, homogeneous germanium oxide thin films with a high content of oxygen vacancies were fabricated. Ultraviolet absorption and oxygen vacancies of the films were investigated as a function of annealing temperature and time. Optical absorption in the 5‐eV region due to the formation of oxygen vacancies is enhanced with increasing annealing temperature and time. The formation energy of oxygen vacancies is calculated to be about 1.0 eV.
Current–Voltage Characteristics of Σ1 Boundaries with and without Cobalt Ions in Niobium‐Doped SrTiO3 Bicrystals
Authors: Yamamoto Takahisa , Hayashi Katsuro , Ikuhara Yuichi , Sakuma Taketo
Published: January 2009

Current–voltage (I–V) characteristics across Σ1 boundaries of Nb‐doped SrTiO3 bicrystals were investigated with a special interest in the effect of an impurity ion, cobalt. The Σ1 boundary with cobalt ions was fabricated by hot‐joining technique after evaporating metallic cobalt onto the (001) plane used for a contact plane. High‐resolution transmission electron microscopy (HREM) study associated with X‐ray energy dispersive spectroscopy (EDS) revealed that cobalt solved and distributed around the Σ1 boundary which was perfectly joined without any second films. It was found that the Σ1 boundary with cobalt ions exhibited a nonlinear I–V relationship while the Σ1 boundary without cobalt ions showed a linear I–V relationship. This result indicates that the presence of cobalt itself at the boundary can form a potential barrier irrespective of grain boundary coherency.
Quality of life, health satisfaction and family impact on caregivers of children with developmental delays
Authors: Hsieh R. L. , Huang H. Y. , Lin M. I. , Wu C. W. , Lee Wen‐Chung
Published: January 2009

Objective  To study the quality of life, health satisfaction and family impact on caregivers of children with developmental delays in Taiwan.

Design  Cross‐sectional study.

Subjects  The caregivers of children with diagnoses of developmental delays recruited from a teaching hospital in northern Taiwan.

Methods  The main caregivers of 48 male and 22 female children with developmental delays were recruited. WHOQOL‐BREF for health‐related quality of life (HRQOL), PedsQL‐Health Satisfaction for health satisfaction, PedsQL‐Family Impact Module and Impact on Family Scale for family impact were evaluated. The correlation of caregivers' HRQOL, health satisfaction and family impact were also studied.

Results  Caregivers in nuclear families had higher health satisfaction scores (78.2 for nuclear families vs. 66.9 for extended families, P < 0.05) when assessed by the PedQL‐Health Satisfaction questionnaire. Children's age was negatively correlated with family impact, including parent (−0.272, P = 0.023), family (−0.262, P = 0.029) and total scores (−0.281, P = 0.018) as assessed using the PedsQL‐Family Impact Module.

Conclusion  A negative relation between impact of burden and child's age suggests that family members gradually adapt to the delayed developmental status in their children as they grow. Caregivers in nuclear families having higher health satisfaction than those in extended families may be due to Chinese cultural effects.
Predator–prey interactions in river networks: comparing shrimp spatial refugia in two drainage basins
Authors: COVICH ALAN P. , CROWL TODD A. , HEIN CATHERINE L. , TOWNSEND MATT J. , MCDOWELL WILLIAM H.
Published: January 2009

1. Analysis of drainage networks provides a framework to evaluate the densities and distributions of prey species relative to locations of their predators. Upstream migration by diadromous shrimp (Atya lanipes and Xiphocaris elongata) during their life cycle provides access to headwater refugia from fish predation, which is intense in estuaries and coastal rivers.

2. We postulate that geomorphic barriers (such as large, steep waterfalls >3.5 m in height), can directly limit the distribution of predatory fishes and, indirectly, affect the densities of their prey (freshwater shrimps) in headwater streams.

3. We compared densities of shrimp in pools above and below waterfalls, in four headwater tributaries in two river basins of the Luquillo Mountains of northeastern Puerto Rico. We measured shrimp densities twice a year over 8 years (1998–2005) in Prieta, Toronja, Bisley 3 and Bisley 5 streams, which differ in drainage network positions relative to steep waterfalls in Río Espíritu Santo and Río Mameyes.

4. Predatory fishes are absent in the Prieta and Toronja pools and present in Bisely 3 and in lower Bisley 5 pools. Atya lanipes and X. elongata rarely occur in the Bisley streams where predatory fishes are present but these shrimps are abundant in Prieta and Toronja, streams lacking predatory fishes.

5. The mean carapace length of X. elongata is longer in pools where fish are present (Bisley 3 and lower Bisley 5) than in pools lacking fish (Prieta, Toronja, Upper Bisley 5). The increased body size is primarily due to significantly longer rostrums of individuals in stream reaches with fish (below waterfall barriers) than in those reaches lacking fish (above waterfall barriers). Rostrum length may be an adaptation to avoid predation by visually feeding fishes.

6. Atya lanipes and X. elongata distributions and densities were predicted primarily by drainage network position relative to the presence or absence of predatory fishes. High, steep waterfalls effectively impeded fish from moving upstream and created a spatial refuge. Xiphocaris elongata may rely on size refugia (longer rostrum) to minimize predation where spatial refugia are lacking.