bluuebunny/crossref_metadata_2025 huggingface dataset:
A combined reflectometry and quartz crystal microbalance with dissipation setup for surface interaction studies
Authors: Wang Guoliang , Rodahl Michael , Edvardsson Malin , Svedhem Sofia , Ohlsson Gabriel , Höök Fredrik , Kasemo Bengt
Published: July 2008

We have developed an instrument for surface interaction studies, which combines a newly invented four detector optical reflectometry setup with quartz crystal microbalance with dissipation (QCM-D) monitoring. The design is such that data from both techniques can be obtained simultaneously on the same sensor surface, with the same signal-to-noise ratio and time resolution, as for the individual techniques. In addition, synchronized information about structural transformations, molecular mass, and the hydration of thin films on solid surfaces can be obtained on the same specimen, as validated by monitoring the formation of supported lipid bilayers on a silica-coated QCM sensor surface. We emphasize that the optical (molecular) mass can be separated from the acoustic mass including hydrodynamically coupled solvent, which means, in turn, that the amount of solvent sensed by the QCM-D technique can be dynamically resolved during adsorption processes. In addition, the advantage/necessity to use four, compared to two, detector reflectometry is emphasized.
The role of the β-phase content on the stimulated emission of poly(9,9-dioctylfluorene) thin films
Authors: Anni M.
Published: July 2008

We investigated the optical gain properties of poly(9,9-dioctylfluorene) thin films as a function of the β-phase content. We demonstrate that the product between the gain cross section and the excited state lifetime of the β-phase is about 3.2 times larger than the glassy-phase one, indicating that the β-phase molecules, for a given pump density, have higher gain than the glassy-phase ones. The dependence of the amplified spontaneous emission threshold on the molecular properties, on the waveguide losses, and on the β-phase content is also quantitatively discussed.
Electron spin resonance studies of P and B codoped Si nanocrystals
Authors: Fujio Kazuyoshi , Fujii Minoru , Sumida Kazuaki , Hayashi Shinji , Fujisawa Masashi , Ohta Hitoshi
Published: July 2008

P- and/or B-doped Si nanocrystals (Si-ncs) embedded in glass matrices were studied by electron spin resonance (ESR) spectroscopy to investigate the origin of strong room-temperature photoluminescence (PL) of n- and p-type impurities codoped Si-ncs below the band-gap energy of bulk Si crystals. It was shown that the intensity and width of the ESR signal depend strongly on impurity concentrations. A clear correlation was observed between the ESR signal width and the PL intensity. The observed correlation suggests that in addition to the geometrical confinement, P and B codoping further localize carriers in Si-ncs, and the strong localization results in the characteristic luminescence properties.
Organic phototransistor based on poly(3-hexylthiophene)/TiO2 nanoparticle composite
Authors: Mok Sheung Man , Yan Feng , Chan Helen L. W.
Published: July 2008

Light sensitive phototransistor based on the composite of poly(3-hexylthiophene) and TiO2 nanoparticles has been developed. The device shows a quick change in channel current under light exposure, which can be attributed to a positive shift of the threshold voltage, while no change in the field effect mobility and off current can be observed. The shift of the threshold voltage is induced by accumulated electrons trapped by the TiO2 nanoparticles in the channel. The photosensitivity of the device has been found to be dependent on the concentration of TiO2 nanoparticles, the incident wavelength and the voltage between the source and drain.
On the scaling of turbulent separating boundary layers
Authors: Lögdberg Ola , Angele Kristian , Alfredsson P. Henrik
Published: July 2008

This study focuses on the mean velocity distribution of turbulent boundary layers near, at, and after separation. The proper mean velocity scaling of the outer region in strong adverse pressure gradients and separated turbulent boundary layers is still under debate and over the years various different velocity scales have been proposed. Here the scaling proposed by Zagarola and Smits [J. Fluid Mech. 373, 33 (1998)] is applied to data from three different separated flows. In all cases the mean velocity defect profiles are self-similar in the region between separation and the position of maximum mean reverse flow. Downstream of the reverse flow maximum, the profiles change, but they are still self-similar within that region. It was also found that the mean velocity defect profiles of all three pressure gradients show similarity in the region between separation and the position of maximum mean reverse flow.
Reduction of thermal conductivity in wafer-bonded silicon
Authors: Liau Z. L. , Danielson L. R. , Fourspring P. M. , Hu L. , Chen G. , Turner G. W.
Published: July 2008

Blocks of silicon up to 3mm thick have been formed by directly bonding stacks of thin wafer chips. These stacks showed significant reductions in the thermal conductivity in the bonding direction. In each sample, the wafer chips were obtained by polishing a commercial wafer to as thin as 36μm, followed by dicing. Stacks whose starting wafers were patterned with shallow dots showed greater reductions in thermal conductivity. Diluted-HF treatment of wafer chips prior to bonding led to the largest reduction of the effective thermal conductivity, by approximately a factor of 50. Theoretical modeling based on restricted conduction through the contacting dots and some conduction across the planar nanometer air gaps yielded good agreement for samples fabricated without the HF treatment.
Magnetic characterization of bulk nanostructured iron oxides
Authors: Morales J. R. , Garay J. E. , Biasini M. , Beyermann W. P.
Published: July 2008

Iron oxide nanopowders were consolidated using a current activated method at varying temperatures. The resulting bulk dense samples with crystal sizes in the nanometric range were found to be mixtures of cubic and hexagonal phases of iron oxides (nanocomposites). Magnetic characterization reveals one abrupt increase, up to 300%, in the magnetization with increasing temperature. The coercivity Hc steps down 300% at this point as well. The transition temperature, T1, is strongly dependent on the size of the nanopowder employed during the sintering. For the sizes of 8 and 40nm we detect T1=(14±2)K and T1=(122±1)K, respectively.
Effect of antimony incorporation on the density, shape, and luminescence of InAs quantum dots
Authors: Chen J. F. , Chiang C. H. , Wu Y. H. , Chang L. , Chi J. Y.
Published: July 2008

This work investigates the surfactant effect on exposed and buried InAs quantum dots (QDs) by incorporating Sb into the QD layers with various Sb beam equivalent pressures (BEPs). Secondary ion mass spectroscopy shows the presence of Sb in the exposed and buried QD layers with the Sb intensity in the exposed layer substantially exceeding that in the buried layer. Incorporating Sb can reduce the density of the exposed QDs by more than two orders of magnitude. However, a high Sb BEP yields a surface morphology with a regular periodic structure of ellipsoid terraces. A good room-temperature photoluminescence (PL) at ∼1600 nm from the exposed QDs is observed, suggesting that the Sb incorporation probably improves the emission efficiency by reducing the surface recombination velocity at the surface of the exposed QDs. Increasing Sb BEP causes a blueshift of the emission from the exposed QDs due to a reduction in the dot height as suggested by atomic force microscopy. Increasing Sb BEP can also blueshift the ∼1300 nm emission from the buried QDs by decreasing the dot height. However, a high Sb BEP yields a quantum well-like PL feature formed by the clustering of the buried QDs into an undulated planar layer. These results indicate a marked Sb surfactant effect that can be used to control the density, shape, and luminescence of the exposed and buried QDs.
Plastic complementary microelectromechanical switches
Authors: Yokota Tomoyuki , Nakano Shintaro , Sekitani Tsuyoshi , Someya Takao
Published: July 2008

We have fabricated plastic complementary microelectromechanical switches by using ink-jet printing technologies. Two vertically stacked regular plastic microelectromechanical switches that are complementary to each other realize the function of an inverter. While rectangular voltage waveforms were periodically applied to the control electrodes in the air, the delay times and durability were examined systematically. The frequency response was 50 Hz for an operation voltage of 60 V. When the number of periodic cycles exceeded 106, the changes in the on resistance of the top and bottom switches were 9% and 43%, respectively.
Solid state organic laser emission at 970nm from dye-doped fluorinated-polyimide planar waveguides
Authors: Yuyama Shun , Nakajima Takahiro , Yamashita Kenichi , Oe Kunishige
Published: July 2008

We have demonstrated near-infrared amplified spontaneous emission and laser emission from fluorinated-polyimide waveguides doped with an organic dye, 5,6-dichloro-2[8-(p-dimethylaminophenyl)-2,4-neopentylene-1,3,5,7-octatetraenyl]-3-ethylbenzothiazolium perchlorate (LDS950). The planar waveguides doped with 1wt% of the dye, 10mm in length and 9.3μm in thickness, have exhibited amplified spontaneous emission and optical gain around 960nm under optical pulse pumping. A good optical gain coefficient of 1.4mm−1 was obtained. Furthermore, by using the cleaved waveguide edges as reflective facets, sharp emission peaks showing laser oscillation at 970nm were observed under the optical pulse pumping. The lasing threshold was 0.22mJ∕cm2. The lasing wavelength of 970nm is the longest for solid state dye-doped polymeric lasers.
Field emission from a single carbon nanofiber at sub 100nm gap
Authors: Sim H. S. , Lau S. P. , Ang L. K. , You G. F. , Tanemura M. , Yamaguchi K. , Zamri M. , Yusop M.
Published: July 2008

The authors report the electron field emission from a single carbon nanofiber (CNF) over a range of anode to CNF tip separations of 20–5500nm. Our results show that the field enhancement factor γ is associated with the electrode separation (S). The modified Miller equation is a reasonable empirical model to describe the behavior of γ, which varies with S over a large range of values. The γ approaches to an asymptotic value of 415 or 1 when S is very large or very small as compared to the length of the CNF, respectively. The maximum field emission current sustained by the single CNF without causing damage was estimated to be as high as 15μA.
Dielectric and piezoelectric properties of (1−x)(Bi1−yLiy)(Sc1−ySby)O3–xPbTiO3 high-temperature relaxor ferroelectric ceramics
Authors: Jiang Yihang , Zhao Yi , Qin Baoquan , Jiang Yuzhi , Shi Wei , Li Lihua , Xiao Dingquan , Zhu Jianguo
Published: July 2008

Bi Sc O 3 – Li Sb O 3 – Pb Ti O 3 solid solutions with perovskite structure were prepared by the conventional mixed oxide method. X-ray diffraction showed that a change in symmetry from rhombohedral to tetragonal as the mole fraction of PbTiO3 larger than 62%. In the vicinity of the morphotropic phase boundary, the ceramics showed enhanced piezoelectric and ferroelectric properties: piezoelectric constant d33=545pC∕N, planar electromechanical coupling factors kp=58%, remnant polarization Pr=28.3μC∕cm2, and the coercive field Ec=1.8kV∕mm, respectively. The temperature of the permittivity maximum (Tmax) increased with increasing measure of frequency, over the range of 300–340°C, and the ceramics show the relaxor ferroelectric features.
“Plug and Play” single photons at 1.3μm approaching gigahertz operation
Authors: Xu Xiulai , Brossard Frederic , Hammura Kiyotaka , Williams David A. , Alloing B. , Li L. H. , Fiore Andrea
Published: July 2008

We report a “plug and play” single photon source, fully integrated with an optical fiber, emitting at 1.3μm. Micropillars were patterned on a single layer InAs quantum dot wafer to guarantee a single pillar per fiber core. The single exciton peak filtered with a tunable optical filter was fed to a Hanbury Brown and Twiss interferometer, and the second order correlation function at zero delay was less than 0.5, indicating single photon emission. The measured decay dynamics under double-pulse excitation show that the single photon device can be operated at speeds greater than 0.5GHz.
Light extraction enhancement of InGaN light-emitting diode by roughening both undoped micropillar-structure GaN and p-GaN as well as employing an omnidirectional reflector
Authors: Horng Ray-Hua , Zheng Xinhe , Hsieh Chuang-Yu , Wuu Dong-Sing
Published: July 2008

Light extraction enhancement of InGaN–GaN light-emitting diode (LED) is demonstrated with double-side roughening both on the p-GaN surface and the micropillar undoped GaN as well as an omnidirectional reflector via patterning sapphire substrate, wafer-bonding, laser lift-off, and chemical wet etching technologies. This device design enhances the light output power up to 77% compared to the conventional LED with a single roughened p-GaN on patterned sapphire substrate at an injection current of 350mA. Due to the employment of Si carrier, the junction temperature measurement at 350mA yields a 46.6°C lower than that of the conventional LEDs.
Strain control of the magnetic anisotropy in (Ga,Mn) (As,P) ferromagnetic semiconductor layers
Authors: Lemaître A. , Miard A. , Travers L. , Mauguin O. , Largeau L. , Gourdon C. , Jeudy V. , Tran M. , George J.-M.
Published: July 2008

A small fraction of phosphorus (up to 10%) was incorporated in ferromagnetic (Ga,Mn)As epilayers grown on a GaAs substrate. P incorporation allows reducing the epitaxial strain or even change its sign, resulting in strong modifications of the magnetic anisotropy. In particular a reorientation of the easy axis toward the growth direction is observed for high P concentration. It offers an interesting alternative to the metamorphic approach, in particular for magnetization reversal experiments where epitaxial defects strongly affect the domain wall propagation.
Relaxation dynamics of NH stretching vibrations of 2-aminopyridine and its dimer in a supersonic beam
Authors: Yamada Yuji , Mikami Naohiko , Ebata Takayuki
Published: July 2008

Picosecond time-resolved IR–UV pump–probe spectroscopy has been carried out to elucidate vibrational energy relaxation (VER) of the NH stretching vibrations of 2-aminopyridine monomer (2AP) and dimer [(2AP)
2
] in supersonic beams. In bare 2AP, intramolecular vibrational energy redistribution (IVR) of the NH vibrations is described by the two-bath mode model, in which the initial vibrational energy flows to the doorway states rapidly (6.5 ps) and then dissipates into the dense bath states with a time constant of ≈20 ps. No clear difference was observed in the IVR lifetime between the symmetric and asymmetric NH
2
stretch modes. In (2AP)
2
, IVR and vibrational predissociation (VP) were involved in VER. It was found that the rate constants of both IVR and VP of the hydrogen-bonded NH stretching vibration are larger than those of the free NH.
Evolution of flowering decisions in a stochastic, density-dependent environment
Authors: Metcalf C. J. E. , Rose K. E. , Childs D. Z. , Sheppard A. W. , Grubb P. J. , Rees M.
Published: July 2008

Demography is central to both ecology and evolution, and characterizing the feedback between ecology and evolution is critical for understanding organisms' life histories and how these might evolve through time. Here, we show how, by combining a range of theoretical approaches with the statistical analysis of individually structured databases, accurate prediction of life history decisions is possible in natural density-regulated populations undergoing large fluctuations in demographic rates from year to year. Our predictions are remarkably accurate and statistically well defined. In addition, we show that the predicted trait values are evolutionarily and convergence stable and that protected polymorphisms are possible.
Development of pulmonary fibrosis through a pathway involving the transcription factor Fra-2/AP-1
Authors: Eferl Robert , Hasselblatt Peter , Rath Martina , Popper Helmut , Zenz Rainer , Komnenovic Vukoslav , Idarraga Maria-Helena , Kenner Lukas , Wagner Erwin F.
Published: July 2008

Studies using genetically modified mice have revealed fundamental functions of the transcription factor Fos/AP-1 in bone biology, inflammation, and cancer. However, the biological role of the Fos-related protein Fra-2 is not well defined
in vivo
. Here we report an unexpected profibrogenic function of Fra-2 in transgenic mice, in which ectopic expression of Fra-2 in various organs resulted in generalized fibrosis with predominant manifestation in the lung. The pulmonary phenotype was characterized by vascular remodeling and obliteration of pulmonary arteries, which coincided with expression of osteopontin, an AP-1 target gene involved in vascular remodeling and fibrogenesis. These alterations were followed by inflammation; release of profibrogenic factors, such as IL-4, insulin-like growth factor 1, and CXCL5; progressive fibrosis; and premature mortality. Genetic experiments and bone marrow reconstitutions suggested that fibrosis developed independently of B and T cells and was not mediated by autoimmunity despite the marked inflammation observed in transgenic lungs. Importantly, strong expression of Fra-2 was also observed in human samples of idiopathic and autoimmune-mediated pulmonary fibrosis. These findings indicate that Fra-2 expression is sufficient to cause pulmonary fibrosis in mice, possibly by linking vascular remodeling and fibrogenesis, and suggest that Fra-2 has to be considered a contributing pathogenic factor of pulmonary fibrosis in humans.
Differential requirements for Alix and ESCRT-III in cytokinesis and HIV-1 release
Authors: Carlton Jez G. , Agromayor Monica , Martin-Serrano Juan
Published: July 2008

The ESCRT machinery functions in topologically equivalent membrane fission events, namely multivesicular body formation, the terminal stages of cytokinesis and HIV-1 release. Here, we show that the ESCRT-III-binding protein Alix is recruited to the midbody of dividing cells through binding Cep55 via an evolutionarily conserved peptide. Disruption of Cep55/Alix/ESCRT-III interactions causes formation of aberrant midbodies and cytokinetic failure, demonstrating an essential role for these proteins in midbody morphology and cell division. We also show that the C terminus of Alix encodes a multimerization activity that is essential for its function in Alix-dependent HIV-1 release and for interaction with Tsg101. Last, we demonstrate that overexpression of Chmp4b and Chmp4c differentially inhibits HIV-1 release and cytokinesis, suggesting possible reasons for gene expansion within the mammalian Class E VPS pathway.
Insights into protein flexibility: The relationship between normal modes and conformational change upon protein–protein docking
Authors: Dobbins Sara E. , Lesk Victor I. , Sternberg Michael J. E.
Published: July 2008

Understanding protein interactions has broad implications for the mechanism of recognition, protein design, and assigning putative functions to uncharacterized proteins. Studying protein flexibility is a key component in the challenge of describing protein interactions. In this work, we characterize the observed conformational change for a set of 20 proteins that undergo large conformational change upon association (>2 Å Cα RMSD) and ask what features of the motion are successfully reproduced by the normal modes of the system. We demonstrate that normal modes can be used to identify mobile regions and, in some proteins, to reproduce the direction of conformational change. In 35% of the proteins studied, a single low-frequency normal mode was found that describes well the direction of the observed conformational change. Finally, we find that for a set of 134 proteins from a docking benchmark that the characteristic frequencies of normal modes can be used to predict reliably the extent of observed conformational change. We discuss the implications of the results for the mechanics of protein recognition.
Protein phosphatase 1 regulates the phosphorylation state of the polarity scaffold Par-3
Authors: Traweger Andreas , Wiggin Giselle , Taylor Lorne , Tate Stephen A. , Metalnikov Pavel , Pawson Tony
Published: July 2008

Phosphorylation of the polarity protein Par-3 by the serine/threonine kinases aPKCζ/ι and Par-1 (EMK1/MARK2) regulates various aspects of epithelial cell polarity, but little is known about the mechanisms by which these posttranslational modifications are reversed. We find that the serine/threonine protein phosphatase PP1 (predominantly the α isoform) binds Par-3, which localizes to tight junctions in MDCKII cells. PP1α can associate with multiple sites on Par-3 while retaining its phosphatase activity. By using a quantitative mass spectrometry-based technique, multiple reaction monitoring, we show that PP1α specifically dephosphorylates Ser-144 and Ser-824 of mouse Par-3, as well as a peptide encompassing Ser-885. Consistent with these observations, PP1α regulates the binding of 14-3-3 proteins and the atypical protein kinase C (aPKC) ζ to Par-3. Furthermore, the induced expression of a catalytically inactive mutant of PP1α severely delays the formation of functional tight junctions in MDCKII cells. Collectively, these results show that Par-3 functions as a scaffold, coordinating both serine/threonine kinases and the PP1α phosphatase, thereby providing dynamic control of the phosphorylation events that regulate the Par-3/aPKC complex.
Crystal structure of the complex between programmed death-1 (PD-1) and its ligand PD-L2
Authors: Lázár-Molnár Eszter , Yan Qingrong , Cao Erhu , Ramagopal Udupi , Nathenson Stanley G. , Almo Steven C.
Published: July 2008

Programmed death-1 (PD-1) is a member of the CD28/B7 superfamily that delivers negative signals upon interaction with its two ligands, PD-L1 or PD-L2. The high-resolution crystal structure of the complex formed by the complete ectodomains of murine PD-1 and PD-L2 revealed a 1:1 receptor:ligand stoichiometry and displayed a binding interface and overall molecular organization distinct from that observed in the CTLA-4/B7 inhibitory complexes. Furthermore, our structure also provides insights into the association between PD-1 and PD-L1 and highlights differences in the interfaces formed by the two PD-1 ligands (PD-Ls) Mutagenesis studies confirmed the details of the proposed PD-1/PD-L binding interfaces and allowed for the design of a mutant PD-1 receptor with enhanced affinity. These studies define spatial and organizational constraints that control the localization and signaling of PD-1/PD-L complexes within the immunological synapse and provide a basis for manipulating the PD-1 pathways for immunotherapy.
Message-passing algorithms for the prediction of protein domain interactions from protein–protein interaction data
Authors: Iqbal Mudassar , Freitas Alex A. , Johnson Colin G. , Vergassola Massimo
Published: July 2008

Motivation: Cellular processes often hinge upon specific interactions among proteins, and knowledge of these processes at a system level constitutes a major goal of proteomics. In particular, a greater understanding of protein–protein interactions can be gained via a more detailed investigation of the protein domain interactions that mediate the interactions of proteins. Existing high-throughput experimental techniques assay protein–protein interactions, yet they do not provide any direct information on the interactions among domains. Inferences concerning the latter can be made by analysis of the domain composition of a set of proteins and their interaction map. This inference problem is non-trivial, however, due to the high level of noise generally present in experimental data concerning protein–protein interactions. This noise leads to contradictions, i.e. the impossibility of having a pattern of domain interactions compatible with the protein–protein interaction map.

Results: We formulate the problem of prediction of protein domain interactions in a form that lends itself to the application of belief propagation, a powerful algorithm for such inference problems, which is based on message passing. The input to our algorithm is an interaction map among a set of proteins, and a set of domain assignments to the relevant proteins. The output is a list of probabilities of interaction between each pair of domains. Our method is able to effectively cope with errors in the protein–protein interaction dataset and systematically resolve contradictions. We applied the method to a dataset concerning the budding yeast Saccharomyces cerevisiae and tested the quality of our predictions by cross-validation on this dataset, by comparison with existing computational predictions, and finally with experimentally available domain interactions. Results compare favourably to those by existing algorithms.

Availability: A C language implementation of the algorithm is available upon request.

Contact:  mi26@kent.ac.uk
The use of meiofauna diversity as an indicator of pollution in harbours
Authors: Moreno Mariapaola , Vezzulli Luigi , Marin Valentina , Laconi Paola , Albertelli Giancarlo , Fabiano Mauro
Published: July 2008

Moreno, M., Vezzulli, L., Marin, V., Laconi, P., Albertelli, G., and Fabiano, M. 2008. The use of meiofauna diversity as an indicator of pollution in harbours. – ICES Journal of Marine Science, 65: 1428–1435. We assessed several meiofaunal indices in sediments of three Mediterranean harbours differing in environmental contamination to evaluate their usefulness as indicators of pollution and to identify those that best described environmental quality. In general, indicators based on meiofaunal taxa demonstrated a significant correlation with the concentration of contaminants, especially the polycyclic aromatic hydrocarbons (PAHs). Nematode genus-based indicators correlated with contaminant concentrations at similar levels of significance, suggesting that a high taxonomic resolution does not improve the information content of meiofauna diversity indicators for assessing the environmental quality in these harbours. Notably, environmental variables that affect meiofaunal and nematode assemblages (e.g. water depth, grain size, and food sources) demonstrated a low spatial and temporal variability in the harbours investigated and did not represent important confounding factors. We conclude that the application of meiofaunal and nematode indices can be a useful tool for assessing the environmental quality of harbour ecosystems.
Phenotypic engineering by reprogramming gene transcription using novel artificial transcription factors in Escherichia coli
Authors: Lee Ju Young , Sung Bong Hyun , Yu Byung Jo , Lee Jun Hyoung , Lee Sang Hee , Kim Mi Sun , Koob Michael D. , Kim Sun Chang
Published: July 2008

Now that many genomes have been sequenced and the products of newly identified genes have been annotated, the next goal is to engineer the desired phenotypes in organisms of interest. For the phenotypic engineering of microorganisms, we have developed novel artificial transcription factors (ATFs) capable of reprogramming innate gene expression circuits in Escherichia coli. These ATFs are composed of zinc finger (ZF) DNA-binding proteins, with distinct specificities, fused to an E. coli cyclic AMP receptor protein (CRP). By randomly assembling 40 different types of ZFs, we have constructed more than 6.4 × 104 ATFs that consist of 3 ZF DNA-binding domains and a CRP effector domain. Using these ATFs, we induced various phenotypic changes in E. coli and selected for industrially important traits, such as resistance to heat shock, osmotic pressure and cold shock. Genes associated with the heat-shock resistance phenotype were then characterized. These results and the general applicability of this platform clearly indicate that novel ATFs are powerful tools for the phenotypic engineering of microorganisms and can facilitate microbial functional genomic studies.
Exploration of Novel Motifs Derived from Mouse cDNA Sequences
Authors: Kawaji Hideya , Schönbach Christian , Matsuo Yo , Kawai Jun , Okazaki Yasushi , Hayashizaki Yoshihide , Matsuda Hideo
Published: July 2008

We performed a systematic maximum density subgraph (MDS) detection of conserved sequence regions to discover new, biologically relevant motifs from a set of 21,050 conceptually translated mouse cDNA (FANTOM1) sequences. A total of 3202 candidate sequences, which shared similar regions over >20 amino acid residues, were screened against known conserved regions listed in Pfam, ProDom, and InterPro. The filtering procedure resulted in 139 FANTOM1 sequences belonging to 49 new motif candidates. Using annotations and multiple sequence alignment information, we removed by visual inspection 42 candidates whose members were found to be false positives because of sequence redundancy, alternative splicing, low complexity, transcribed retroviral repeat elements contained in the region of the predicted open reading frame, and reports in the literature. The remaining seven motifs have been expanded by hidden Markov model (HMM) profile searches of SWISS-PROT/TrEMBL from 28 FANTOM1 sequences to 164 members and analyzed in detail on sequence and structure level to elucidate the possible functions of motifs and members. The novel and conserved motif MDS00105 is specific for the mammalian inhibitor of growth (ING) family. Three submotifs MDS00105.1–3 are specific for ING1/ING1L, ING1-homolog, and ING3 subfamilies. The motif MDS00105 together with a PHD finger domain constitutes a module for ING proteins. Structural motif MDS00113 represents a leucine zipper-like motif. Conserved motif MDS00145 is a novel 1-acyl-SN-glycerol-3-phosphate acyltransferase (AGPAT) submotif containing a transmembrane domain that distinguishes AGPAT3 and AGPAT4 from all other acyltransferase domain-containing proteins. Functional motif MDS00148 overlaps with the kazal-type serine protease inhibitor domain but has been detected only in an extracellular loop region of solute carrier 21 (SLC21) (organic anion transporters) family members, which may regulate the specificity of anion uptake. Our motif discovery not only aided in the functional characterization of new mouse orthologs for potential drug targets but also allowed us to predict that at least 16 other new motifs are waiting to be discovered from the current SWISS-PROT/TrEMBL database.
A Quantitative Trait Locus Influencing Anxiety in the Laboratory Rat
Authors: Fernández-Teruel Alberto , Escorihuela Rosa M. , Gray Jeffrey A. , Aguilar Raúl , Gil Luis , Giménez-Llort Lydia , Tobeña Adolf , Bhomra Amarjit , Nicod Alison , Mott Richard , Driscoll Peter , Dawson Gerard R. , Flint Jonathan
Published: July 2008

A critical test for a gene that influences susceptibility to fear in animals is that it should have a consistent pattern of effects across a broad range of conditioned and unconditioned models of anxiety. Despite many years of research, definitive evidence that genetic effects operate in this way is lacking. The limited behavioral test regimes so far used in genetic mapping experiments and the lack of suitable multivariate methodologies have made it impossible to determine whether the quantitative trait loci (QTL) detected to date specifically influence fear-related traits. Here we report the first multivariate analysis to explore the genetic architecture of rodent behavior in a battery of animal models of anxiety. We have mapped QTLs in an F2 intercross of two rat strains, the Roman high and low avoidance rats, that have been selectively bred for differential response to fear. Multivariate analyses show that one locus, on rat chromosome 5, influences behavior in different models of anxiety. The QTL influences two-way active avoidance, conditioned fear, elevated plus maze, and open field activity but not acoustic startle response or defecation in a novel environment. The direction of effects of the QTL alleles and a coincidence between the behavioral profiles of anxiolytic drug and genetic action are consistent with the QTL containing at least one gene with a pleiotropic action on fear responses. As the neural basis of fear is conserved across species, we suggest that the QTL may have relevance to trait anxiety in humans.
An Integrated Computational and Laboratory Approach for Selective Amplification of mRNAs Containing the Adenylate Uridylate-Rich Element Consensus Sequence
Authors: Khabar Khalid S.A. , Dhalla Mohammed , Bakheet Tala , Sy Cheikh , al-Haj Latifa
Published: July 2008

Messenger RNAs that have the stability determinants, adenylate uridylate-rich elements (AREs), in their 3′ untranslated region (UTR) code for key products that regulate early and transient biological responses. We used a computational laboratory approach for amplification of large, including full-length, protein-coding regions for ARE genes. Statistical analysis of the initiation regions in the 5′ UTR of ARE-mRNAs was performed. Accordingly, several 5′ primers and a single universal 3′ primer that targeted the initiation consensuses and ARE regions, respectively, were designed. Using optimized conditions, the primers were able to enrich and amplify large protein-coding regions for the ARE gene family. The selective amplification of ARE cDNAs was verified using specific polymerase chain reactions (PCRs) to known ARE mRNA molecules and monitoring the abundance of the non-ARE β-actin signal. A mini-library from the amplified ARE products was constructed for further confirmation of ARE selection. Distinct ARE amplified cDNA pools were selectively generated by distinct 5′ primers. The biological utility of the method was shown with differential display. The up-regulation of several ARE-mRNAs, including the full-length coding region of the small inducible cytokine A4(SCYA4)gene, was shown in endotoxin-stimulated monocytic cells. The integrated computational and laboratory approach should lead to enhanced capability for discovery and expression analysis of early and transient response genes.
Oligonucleotide Arrays for High-Throughput SNPs Detection in the MHC Class I Genes: HLA-B as a Model System
Authors: Guo Zhen , Gatterman Mark S. , Hood Lee , Hansen John A. , Petersdorf Effie W.
Published: July 2008

A simple and efficient oligonucleotide array was developed to identify single nucleotide polymorphisms (SNPs) encoded within the highly polymorphic human major histocompatibility complex (MHC) using HLA-B as a model system. A total of 137 probes were designed to represent all known polymorphisms encoded in exons 2 and 3. PCR products were amplified from human genomic DNA and allowed to hybridize with the oligonucleotide array. Hybridization was detected by fluorescence scanning, and HLA-B alleles were assigned by quantitative analysis of the hybridization results. Variables known to influence the specificity of hybridization, such as oligonucleotide probe size, spacer length, surface density, hybridization conditions, and array uniformity and stability were studied. The efficiency and specificity of identifying HLA-B SNPs using the oligonucleotide arrays was evaluated by blinded analysis of 100 samples from unrelated individuals representing all HLA-B phenotypes. The oligonucleotide array method described in this paper provides unambiguous detection of complex heterozygous SNP combinations. This methodological approach may be applied to other highly polymorphic gene systems.
In Silico Prediction of Scaffold/Matrix Attachment Regions in Large Genomic Sequences
Authors: Frisch Matthias , Frech Kornelie , Klingenhoff Andreas , Cartharius Kerstin , Liebich Ines , Werner Thomas
Published: July 2008

Scaffold/matrix attachment regions (S/MARs) are essential regulatory DNA elements of eukaryotic cells. They are major determinants of locus control of gene expression and can shield gene expression from position effects. Experimental detection of S/MARs requires substantial effort and is not suitable for large-scale screening of genomic sequences. In silico prediction of S/MARs can provide a crucial first selection step to reduce the number of candidates. We used experimentally defined S/MAR sequences as the training set and generated a library of new S/MAR-associated, AT-rich patterns described as weight matrices. A new tool calledSMARTestwas developed that identifies potential S/MARs by performing a density analysis based on the S/MAR matrix library (http://www.genomatix.de/cgi-bin/smartest_pd/smartest.pl). S/MAR predictions were evaluated by using six genomic sequences from animal and plant for which S/MARs and non-S/MARs were experimentally mapped.SMARTestreached a sensitivity of 38% and a specificity of 68%. In contrast to previous algorithms, theSMARTestapproach does not depend on the sequence context and is suitable to analyze long genomic sequences up to the size of whole chromosomes. To demonstrate the feasibility of large-scale S/MAR prediction, we analyzed the recently published chromosome 22 sequence and found 1198 S/MAR candidates.
Computational Comparison of Human Genomic Sequence Assemblies for a Region of Chromosome 4
Authors: Semple Colin A.M. , Morris Stewart W. , Porteous David J. , Evans Kathryn L.
Published: July 2008

Much of the available human genomic sequence data exist in a fragmentary draft state following the completion of the initial high-volume sequencing performed by the International Human Genome Sequencing Consortium (IHGSC) and Celera Genomics (CG). We compared six draft genome assemblies over a region of chromosome 4p (D4S394–D4S403), two consecutive releases by the IHGSC at University of California, Santa Cruz (UCSC), two consecutive releases from the National Centre for Biotechnology Information (NCBI), the public release from CG, and a hybrid assembly we have produced using IHGSC and CG sequence data. This region presents particular problems for genomic sequence assembly algorithms as it contains a large tandem repeat and is sparsely covered by draft sequences. The six assemblies differed both in terms of their relative coverage of sequence data from the region and in their estimated rates of misassembly. The CG assembly method attained the lowest level of misassembly, whereas NCBI and UCSC assemblies had the highest levels of coverage. All assemblies examined included <60% of the publicly available sequence from the region. At least 6% of the sequence data within the CG assembly for the D4S394–D4S403 region was not present in publicly available sequence data. We also show that even in a problematic region, existing software tools can be used with high-quality mapping data to produce genomic sequence contigs with a low rate of rearrangements.

[All sequence accessions for the genomic sequence assemblies analyzed and the data sets used to assess coverage and rates of misassembly are available from http://www.ed.ac.uk/∼csemple.]
Polymorphisms and the Differential Antiviral Activity of the Chicken Mx Gene
Authors: Ko Jae-Hong , Jin Hee-Kyung , Asano Atsushi , Takada Ayato , Ninomiya Ai , Kida Hiroshi , Hokiyama Hironao , Ohara Mutsuo , Tsuzuki Masaoki , Nishibori Masahide , Mizutani Makoto , Watanabe Tomomasa
Published: July 2008

The nucleotide sequence of chicken Mx cDNA was reported earlier using the White Leghorn breed in Germany, but it showed no enhanced resistance to viruses. In this study, the nucleotide sequences of chicken Mx cDNA were determined in many breeds. A total of 25 nucleotide substitutions, of which 14 were deduced to cause amino acid exchanges, were detected, suggesting that the chicken Mxgene is very polymorphic. Transfected cell clones expressing chickenMx mRNA were established after the Mx cDNA was constructed with an expression vector and introduced into mouse 3T3 cells, and the Mx genes from some breeds were demonstrated to confer positive antiviral responses to influenza virus and vesicular stomatitis virus. On the basis of the comparison among the antiviral activities associated with many Mx variations, a specific amino acid substitution at position 631 (Ser to Asn) was considered to determine the antivirally positive or negative Mx gene. Thus, a single amino acid substitution influences the antiviral activity of Mx in domesticated chickens.
Extraction of Functional Binding Sites from Unique Regulatory Regions: The Drosophila Early Developmental Enhancers
Authors: Papatsenko Dmitri A. , Makeev Vsevolod J. , Lifanov Alex P. , Régnier Mireille , Nazina Anna G. , Desplan Claude
Published: July 2008

The early developmental enhancers of Drosophila melanogaster comprise one of the most sophisticated regulatory systems in higher eukaryotes. An elaborate code in their DNA sequence translates both maternal and early embryonic regulatory signals into spatial distribution of transcription factors. One of the most striking features of this code is the redundancy of binding sites for these transcription factors (BSTF). Using this redundancy, we explored the possibility of predicting functional binding sites in a single enhancer region without any prior consensus/matrix description or evolutionary sequence comparisons. We developed a conceptually simple algorithm,Scanseq, that employs an original statistical evaluation for identifying the most redundant motifs and locates the position of potential BSTF in a given regulatory region. To estimate the biological relevance of our predictions, we built thorough literature-based annotations for the best-known Drosophiladevelopmental enhancers and we generated detailed distribution maps for the most robust binding sites. The high statistical correlation between the location of BSTF in these experiment-based maps and the location predicted in silico by Scanseqconfirmed the relevance of our approach. We also discuss the definition of true binding sites and the possible biological principles that govern patterning of regulatory regions and the distribution of transcriptional signals.
High-Density Cell Microarrays for Parallel Functional Determinations
Authors: Xu C. Wilson
Published: July 2008

Whole-genome sequencing projects have generated a wealth of gene sequences from a variety of organisms. A major challenge is to rapidly uncover gene regulatory circuits and their functional manifestations at the cellular level. Here we report the coupled fabrication of nanocraters ranging in size from 100 pL to 1.5 nL on permeable membranes for culturing cells. Using this approach, we developed bacterial and yeast cell microarrays that allowed phenotypic determinations of gene activities and drug targets on a large scale. Cell microarrays will therefore be a particularly useful tool for studying phenotypes of gene activities on a genome-wide scale.
Combining Mouse Congenic Strains and Microarray Gene Expression Analyses to Study a Complex Trait: The NOD Model of Type 1 Diabetes
Authors: Eaves Iain A. , Wicker Linda S. , Ghandour Ghassan , Lyons Paul A. , Peterson Laurence B. , Todd John A. , Glynne Richard J.
Published: July 2008

Combining congenic mapping with microarray expression profiling offers an opportunity to establish functional links between genotype and phenotype for complex traits such as type 1 diabetes (T1D). We used high-density oligonucleotide arrays to measure the relative expression levels of >39,000 genes and ESTs in the NOD mouse (a murine model of T1D and other autoimmune conditions), four NOD-derived diabetes-resistant congenic strains, and two nondiabetic control strains. We developed a simple, yet general, method for measuring differential expression that provides an objective assessment of significance and used it to identify >400 gene expression differences and eight new candidates for theIdd9.1locus. We also discovered a potential early biomarker for autoimmune hemolytic anemia that is based on different levels of erythrocyte-specific transcripts in the spleen. Overall, however, our results suggest that the dramatic disease protection conferred by sixIddloci (Idd3,Idd5.1, Idd5.2, Idd9.1, Idd9.2, andIdd9.3) cannot be rationalized in terms of global effects on the noninduced immune system. They also illustrate the degree to which regulatory systems appear to be robust to genetic variation. These observations have important implications for the design of future microarray-based studies in T1D and, more generally, for studies that aim to combine genome-wide expression profiling and congenic mapping.

[The supplemental research data accompanying this article are available through the authors' web site (http://www-gene.cimr.cam.ac.uk/todd/), and the array data have been submitted to the GEO data repository (http://www.ncbi.nlm.nih.gov/geo/) under accession no. GSE11]
Novel Fluorescence Labeling and High-Throughput Assay Technologies for In Vitro Analysis of Protein Interactions
Authors: Doi Nobuhide , Takashima Hideaki , Kinjo Masataka , Sakata Kyoko , Kawahashi Yuko , Oishi Yuko , Oyama Rieko , Miyamoto-Sato Etsuko , Sawasaki Tatsuya , Endo Yaeta , Yanagawa Hiroshi
Published: July 2008

We developed and tested a simple method for fluorescence labeling and interaction analysis of proteins based on a highly efficient in vitro translation system combined with high-throughput technologies such as microarrays and fluorescence cross-correlation spectroscopy (FCCS). By use of puromycin analogs linked to various fluorophores through a deoxycytidylic acid linker, a single fluorophore can be efficiently incorporated into a protein at the carboxyl terminus during in vitro translation. We confirmed that the resulting fluorescently labeled proteins are useful for probing protein–protein and protein–DNA interactions by means of pulldown assay, DNA microarrays, and FCCS in model experiments. These fluorescence assay systems can be easily extended to highly parallel analysis of protein interactions in studies of functional genomics.

[Online supplementary material available at http://www.genome.org.]
GFScan: A Gene Family Search Tool at Genomic DNA Level
Authors: Xuan Zhenyu , McCombie W. Richard , Zhang Michael Q.
Published: July 2008

We have developed GFScan (GeneFamily Scan), a tool that identifies members of a gene family by searching genomic DNA sequences with genomic DNA motifs (or matrices) that are representative of the family. We have tested GFScan on four human gene families including the neurotransmitter-gated ion-channels (NGIC) family, the carbonic anhydrases (CA) family, the Dbl homology (DH) domain family, and the ETS-domain family. All known members of these families with motifs mapped to sequenced genomic DNA regions were found, whereas some novel genomic locations were also found to match the motifs, which may indicate new members in these families. Compared with other methods,GFScan recognized all true positives with much fewer false positives. We also showed that motifs constructed based on human genes could be used to search the mouse genome to identify orthologous family members in mouse. This program is available athttp://www.cshl.org/mzhanglab/.

[The following individuals and institutions kindly provided reagents, samples or unpublished information as indicated in the paper: J. Maddock and Celera Genomics.]