bluuebunny/crossref_metadata_2025 huggingface dataset:
Stress-induced mass detection with a micromechanical/nanomechanical silicon resonator
Authors: Ono Takahito , Esashi Masayoshi
Published: September 2005

The potential ability of micromechanical/nanomechanical silicon resonators with thicknesses of 500 and 146 nm to detect mass and charge in an ion attachment is investigated in vacuum. Low-energy ions are generated by an ionizer and filtered by a quadrupole mass filter. The vibration of the resonator is measured using a laser Doppler vibrometer, which self-oscillates at its fundamental resonant frequency by feedback-controlled electrostatic actuation. The vibration amplitude is kept at a constant with the auto gain control of the feedback loop. The attachment of ions on the one side of the resonator induces the surface stress, resulting in the change of the resonant frequency. Also the feedback gain that keeps the amplitude at a constant changes due to the charge deposition. The measurement of the mass-induced stress of 9.7×10−7N∕m that resulted from a mass attachment smaller than 69 Zg is demonstrated using the 146-nm-thick silicon resonator.
Parallel-field electrorheological clutch: Enhanced high shear rate performance
Authors: Liu Liyu , Huang Xixiang , Shen Cai , Liu Zhengyou , Shi Jing , Wen Weijia , Sheng Ping
Published: September 2005

We present an electrorheological (ER) fluid cylindrical clutch which achieves stable shear stress at high shear rate, and demonstrates superior performance compared with the traditional ER clutches. The design is realized by employing alternate-stripe electrodes on the inner cylinder, with either dielectric or metallic outer rotor. The alternate stripe electrodes generate electric fields with a component parallel to the shearing direction, so that ER particles can form chain structures parallel to shear and thereby bring significant enhanced device performance at a high shear rate. Differences due to the use of dielectric or metallic outer rotor are shown to be compatible with expectations based on simulated electric-field patterns.
Surface morphology of annealed titanium /silicon bilayer in the presence of oxygen
Authors: Ilango S. , Raghavan G. , Kamruddin M. , Bera Santanu , Tyagi A. K.
Published: September 2005

The evolution of surface morphology and chemical composition of vacuum-annealed titanium films deposited on Si(111) substrate with native oxide is investigated. We show that changes in topography and chemical composition of the surface are related to the simultaneous transport of Si and oxygen. The elucidation of this process is done through a combined use of atomic force microscopy, scanning spreading resistance imaging, x-ray photoelectron spectroscopy, and secondary ion mass spectrometry depth profiling. Coalescence of TiO2 columnar grains formed on the silicide surface results in the coarsening of the surface. Variations in root-mean-square roughness of the surface oxide in the presence of the silicide is compared with that of pure titanium oxide for similar heat-treatment conditions.
Intraband absorption of doped GaN∕AlN quantum dots at telecommunication wavelengths
Authors: Tchernycheva M. , Nevou L. , Doyennette L. , Helman A. , Colombelli R. , Julien F. H. , Guillot F. , Monroy E. , Shibata T. , Tanaka M.
Published: September 2005

We report the Stranski–Krastanov growth of Si-doped GaN∕AlN quantum dot superlattices displaying conduction-band interlevel absorption at telecommunication wavelengths. By adjusting the growth conditions, quantum dots with a height of 0.5–1 nm in the density range of 0.1×1012–3×1012cm−2 can be synthesized. All of the samples exhibit room-temperature interlevel absorptions in the 1.41–1.54μm wavelength range. The full width at half maximum of the observed intraband absorptions is as small as 88 meV. We also observe residual intraband absorption for nominally undoped samples. We attribute this effect to the detrapping of electrons in the AlN barriers and subsequent capture in the dots.
Direct observation of domain-wall pinning at nanoscale constrictions
Authors: Kläui M. , Ehrke H. , Rüdiger U. , Kasama T. , Dunin-Borkowski R. E. , Backes D. , Heyderman L. J. , Vaz C. A. F. , Bland J. A. C. , Faini G. , Cambril E. , Wernsdorfer W.
Published: September 2005

In a combined experimental and numerical study, we determine the details of the pinning of domain walls at constrictions in permalloy nanostructures. Using high spatial-resolution (<10nm) electron holography, we image the spin structure of geometrically confined head-to-head domain walls at constrictions. Low-temperature magnetoresistance measurements are used to systematically ascertain the domain-wall depinning fields in constrictions down to 35 nm width. The depinning fields increase from 60 to 335 Oe with decreasing constriction width and depend on the wall spin structure. The energy barrier to depin the wall from the constriction is quantitatively determined and comparison with the depinning field strength allows us to gauge the energy barrier height of the pinning potential.
Negative refraction of left-handed behavior in porous alumina with infiltrated silver at an optical wavelength
Authors: Ao Xianyu , He Sailing
Published: September 2005

Porous alumina with infiltrated silver is suggested to achieve a negative refraction of left-handed behavior at an optical wavelength. Numerical simulations of subwavelength focusing by a slab lens are performed for both H and E polarizations. Beam refraction by a wedge is also simulated to verify the left-handed behavior.
Syntheses, Structures, Properties, and Theoretical Studies of d10 Metal Complexes of Ethylenediamine
Authors: Chen Wen-Tong , Wang Ming-Sheng , Cai Li-Zhen , Guo Guo-Cong , Huang Jin-Shun
Published: September 2005

Four new tris(ethylenediamine)-chelated metal complexes [Zn(en)3]I2·0.5en (1), [Cd(en)3]Cl2·H2O (2), [Cd(en)3]Br2 (3), and [Hg(en)3]Cl2 (4) have been synthesized by solvothermal reactions. The complexes contain discrete [M(en)3]2+ (M = Zn, Cd, Hg) cations and halide anions. The Zn2+ and Cd2+ ions are six-coordinated by three ethylenediamine molecules to form octahedra, while the Hg2+ ion has a trigonal prism coordination geometry. These complexes all display fluorescent properties in the blue range, which are attributed to a ligand-to-metal charge-transfer mechanism according to molecular orbital calculations. The solid-state diffuse reflectance spectra show that 1–4 are wide band-gap semiconductors. IR and thermogravimetric analyses for 1–4 are also presented in this paper.
Whole genome sequence of
Staphylococcus saprophyticus
reveals the pathogenesis of uncomplicated urinary tract infection
Authors: Kuroda Makoto , Yamashita Atsushi , Hirakawa Hideki , Kumano Miyuki , Morikawa Kazuya , Higashide Masato , Maruyama Atsushi , Inose Yumiko , Matoba Kimio , Toh Hidehiro , Kuhara Satoru , Hattori Masahira , Ohta Toshiko
Published: September 2005

Staphylococcus saprophyticus
is a uropathogenic
Staphylococcus
frequently isolated from young female outpatients presenting with uncomplicated urinary tract infections. We sequenced the whole genome of
S. saprophyticus
type strain ATCC 15305, which harbors a circular chromosome of 2,516,575 bp with 2,446 ORFs and two plasmids. Comparative genomic analyses with the strains of two other species,
Staphylococcus aureus
and
Staphylococcus epidermidis
, as well as experimental data, revealed the following characteristics of the
S. saprophyticus
genome.
S. saprophyticus
does not possess any virulence factors found in
S. aureus
, such as coagulase, enterotoxins, exoenzymes, and extracellular matrix-binding proteins, although it does have a remarkable paralog expansion of transport systems related to highly variable ion contents in the urinary environment. A further unique feature is that only a single ORF is predictable as a cell wall-anchored protein, and it shows positive hemagglutination and adherence to human bladder cell associated with initial colonization in the urinary tract. It also shows significantly high urease activity in
S. saprophyticus
. The uropathogenicity of
S. saprophyticus
can be attributed to its genome that is needed for its survival in the human urinary tract by means of novel cell wall-anchored adhesin and redundant uro-adaptive transport systems, together with urease.
Initial electron donor and acceptor in isolated Photosystem II reaction centers identified with femtosecond mid-IR spectroscopy
Authors: Groot Marie Louise , Pawlowicz Natalia P. , van Wilderen Luuk J. G. W. , Breton Jacques , van Stokkum Ivo H. M. , van Grondelle Rienk
Published: September 2005

Despite the apparent similarity between the plant Photosystem II reaction center (RC) and its purple bacterial counterpart, we show in this work that the mechanism of charge separation is very different for the two photosynthetic RCs. By using femtosecond visible-pump–mid-infrared probe spectroscopy in the region of the chlorophyll ester and keto modes, between 1,775 and 1,585 cm
–1
, with 150-fs time resolution, we show that the reduction of pheophytin occurs on a 0.6- to 0.8-ps time scale, whereas P
+
, the precursor state for water oxidation, is formed after ≈6 ps. We conclude therefore that in the Photosystem II RC the primary charge separation occurs between the “accessory chlorophyll” Chl
D1
and the pheophytin on the so-called active branch.
Allostery of actin filaments: Molecular dynamics simulations and coarse-grained analysis
Authors: Chu Jhih-Wei , Voth Gregory A.
Published: September 2005

The structural and mechanical properties of monomeric actin (G-actin), the trimer nucleus, and actin filaments (F-actins) are determined as a function of the conformation of the DNase I-binding loop (DB loop) by using all-atom molecular dynamics simulations and coarse-grained (CG) analysis. Recent x-ray structures of ADP-bound G-actin (G-ADP) by Otterbeinet al.[Otterbein, L. R., Graceffa, P. & Dominguez, R. (2001)Science293, 708–711] and ATP-bound G-actin (G-ATP) by Graceffa and Dominguez [Graceffa, P. & Dominguez, R. (2003)J. Biol. Chem.278, 34172–34180] indicate that the DB loop of actin does not have a well defined secondary structure in the ATP state but folds into an α-helix in the ADP state. MD simulations and CG analysis indicate that such a helical DB loop significantly weakens the intermonomer interactions of actin assemblies and thus leads to a wider, shorter, and more disordered filament. The computed persistence lengths of F-actin composed of G-ATP (16 μm) and of G-ADP (8.5 μm) agree well with the experimental values for the two states. Therefore, the loop-to-helix transition of the DB loop may be one of the factors that lead to the changes in structural and mechanical properties of F-actin after ATP hydrolysis. This result may provide a direct connection between the conformational changes of an actin monomer and the structural and mechanical properties of the cytoskeleton. The information provided by MD simulations also helps to understand the possible origin of the special features of actin dynamics.
Crystal structures of human glutaminyl cyclase, an enzyme responsible for protein N-terminal pyroglutamate formation
Authors: Huang Kai-Fa , Liu Yi-Liang , Cheng Wei-Ju , Ko Tzu-Ping , Wang Andrew H.-J.
Published: September 2005

N-terminal pyroglutamate (pGlu) formation from its glutaminyl (or glutamyl) precursor is required in the maturation of numerous bioactive peptides. The aberrant formation of pGlu may be related to several pathological processes, such as osteoporosis and amyloidotic diseases. This N-terminal cyclization reaction, once thought to proceed spontaneously, is greatly facilitated by the enzyme glutaminyl cyclase (QC). To probe this important but poorly understood modification, we present here the structure of human QC in free form and bound to a substrate and three imidazole-derived inhibitors. The structure reveals an α/β scaffold akin to that of two-zinc exopeptidases but with several insertions and deletions, particularly in the active-site region. The relatively closed active site displays alternate conformations due to the different indole orientations of Trp-207, resulting in two substrate (glutamine
t
-butyl ester)-binding modes. The single zinc ion in the active site is coordinated to three conserved residues and one water molecule, which is replaced by an imidazole nitrogen upon binding of the inhibitors. Together with structural and kinetic analyses of several active-site-mutant enzymes, a catalysis mechanism of the formation of protein N-terminal pGlu is proposed. Our results provide a structural basis for the rational design of inhibitors against QC-associated disorders.
Biological function of the vaccinia virus Z-DNA-binding protein E3L: Gene transactivation and antiapoptotic activity in HeLa cells
Authors: Kwon Jin-Ah , Rich Alexander
Published: August 2005

The vaccinia virus (VV) E3L protein is essential for virulence and has anti-apoptotic activity. In mice, Z-DNA-binding activity of the N-terminal domain of E3L (Zα) is necessary for viral lethality. Here, we report that inhibition of hygromycin-B-induced apoptosis in HeLa cells depends on Z-DNA binding of the E3L Zα domain. Z-DNA-binding domains of other proteins are equally effective in blocking apoptosis. Using a transient reporter assay, we demonstrate transactivation of human IL-6, nuclear factor of activated T cells (NF-AT), and
p53
genes by E3L. This activation also requires Z-DNA binding of the N-terminal domain of E3L. Overall, this work suggests that the important role of E3L in VV pathogenesis involves modulating expression of host cellular genes at the transcriptional level and inhibiting apoptosis of host cells through Z-DNA binding.
Microarray Analyses of Gene Expression during Chondrocyte Differentiation Identifies Novel Regulators of Hypertrophy
Authors: James Claudine G. , Appleton C. Thomas G. , Ulici Veronica , Underhill T. Michael , Beier Frank
Published: September 2005

Ordered chondrocyte differentiation and maturation is required for normal skeletal development, but the intracellular pathways regulating this process remain largely unclear. We used Affymetrix microarrays to examine temporal gene expression patterns during chondrogenic differentiation in a mouse micromass culture system. Robust normalization of the data identified 3300 differentially expressed probe sets, which corresponds to 1772, 481, and 249 probe sets exhibiting minimum 2-, 5-, and 10-fold changes over the time period, respectively. GeneOntology annotations for molecular function show changes in the expression of molecules involved in transcriptional regulation and signal transduction among others. The expression of identified markers was confirmed by RT-PCR, and cluster analysis revealed groups of coexpressed transcripts. One gene that was up-regulated at later stages of chondrocyte differentiation was Rgs2. Overexpression of Rgs2 in the chondrogenic cell line ATDC5 resulted in accelerated hypertrophic differentiation, thus providing functional validation of microarray data. Collectively, these analyses provide novel information on the temporal expression of molecules regulating endochondral bone development.
Dynamic Alterations in Gene Expression after Wnt-mediated Induction of Avian Neural Crest
Authors: Taneyhill Lisa A. , Bronner-Fraser Marianne
Published: September 2005

The Wnt signaling pathway is important in the formation of neural crest cells in many vertebrates, but the downstream targets of neural crest induction by Wnt are largely unknown. Here, we examined quantitative changes in gene expression regulated by Wnt-mediated neural crest induction using quantitative PCR (QPCR). Induction was recapitulated in vitro by adding soluble Wnt to intermediate neural plate tissue cultured in collagen, and induced versus control tissue were assayed using gene-specific primers at times corresponding to premigratory (18 and 24 h) or early (36 h) stages of crest migration. The results show that Wnt signaling up-regulates in a distinct temporal pattern the expression of several genes normally expressed in the dorsal neural tube (slug, Pax3, Msx1, FoxD3, cadherin 6B) at “premigratory” stages. While slug is maintained in early migrating crest cells, Pax3, FoxD3, Msx1 and cadherin 6B all are down-regulated by the start of migration. These results differ from the temporal profile of these genes in response to the addition of recombinant BMP4, where gene expression seems to be maintained. Interestingly, expression of rhoB is unchanged or even decreased in response to Wnt-mediated induction at all times examined, though it is up-regulated by BMP signals. The temporal QPCR profiles in our culture paradigm approximate in vivo expression patterns of these genes before neural crest migration, and are consistent with Wnt being an initial neural crest inducer with additional signals like BMP and other factors maintaining expression of these genes in vivo. Our results are the first to quantitatively describe changes in gene expression in response to a Wnt or BMP signal during transformation of a neural tube cell into a migratory neural crest cell.
Taz1, an Outer Mitochondrial Membrane Protein, Affects Stability and Assembly of Inner Membrane Protein Complexes: Implications for Barth Syndrome
Authors: Brandner Katrin , Mick David U. , Frazier Ann E. , Taylor Rebecca D. , Meisinger Chris , Rehling Peter
Published: September 2005

The Saccharomyces cerevisiae Taz1 protein is the orthologue of human Tafazzin, a protein that when inactive causes Barth Syndrome (BTHS), a severe inherited X-linked disease. Taz1 is a mitochondrial acyltransferase involved in the remodeling of cardiolipin. We show that Taz1 is an outer mitochondrial membrane protein exposed to the intermembrane space (IMS). Transport of Taz1 into mitochondria depends on the receptor Tom5 of the translocase of the outer membrane (TOM complex) and the small Tim proteins of the IMS, but is independent of the sorting and assembly complex (SAM). TAZ1 deletion in yeast leads to growth defects on nonfermentable carbon sources, indicative of a defect in respiration. Because cardiolipin has been proposed to stabilize supercomplexes of the respiratory chain complexes III and IV, we assess supercomplexes in taz1Δ mitochondria and show that these are destabilized in taz1Δ mitochondria. This leads to a selective release of a complex IV monomer from the III2IV2supercomplex. In addition, assembly analyses of newly imported subunits into complex IV show that incorporation of the complex IV monomer into supercomplexes is affected in taz1Δ mitochondria. We conclude that inactivation of Taz1 affects both assembly and stability of respiratory chain complexes in the inner membrane of mitochondria.
Cytosolic Stress Reduces Degradation of Connexin43 Internalized from the Cell Surface and Enhances Gap Junction Formation and Function
Authors: VanSlyke Judy K. , Musil Linda S.
Published: September 2005

The protein constituents of gap junctions, connexins, have a rapid basal rate of degradation even after transport to the cell surface. We have used cell surface biotinylation to label gap junction-unassembled plasma membrane pools of connexin43 (Cx43) and show that their degradation is inhibited by mild hyperthermia, oxidative stress, and proteasome inhibitors. Cytosolic stress does not perturb endocytosis of biotinylated Cx43, but instead it seems to interfere with its targeting and/or transport to the lysosome, possibly by increasing the level of unfolded protein in the cytosol. This allows more Cx43 molecules to recycle to the cell surface, where they are assembled into long-lived, functional gap junctions in otherwise gap junction assembly-inefficient cells. Cytosolic stress also slowed degradation of biotinylated Cx43 in gap junction assembly-efficient normal rat kidney fibroblasts, and reduced the rate at which gap junctions disappeared from cell interfaces under conditions that blocked transport of nascent connexin molecules to the plasma membrane. These data demonstrate that degradation from the cell surface can be down-regulated by physiologically relevant forms of stress. For connexins, this may serve to enhance or preserve gap junction-mediated intercellular communication even under conditions in which protein synthesis and/or intracellular transport are compromised.
The Cysteine-rich Domain of the Secreted Proprotein Convertases PC5A and PACE4 Functions as a Cell Surface Anchor and Interacts with Tissue Inhibitors of Metalloproteinases
Authors: Nour Nadia , Mayer Gaétan , Mort John S. , Salvas Alexandre , Mbikay Majambu , Morrison Charlotte J. , Overall Christopher M. , Seidah Nabil G.
Published: September 2005

The proprotein convertases PC5, PACE4 and furin contain a C-terminal cysteine-rich domain (CRD) of unknown function. We demonstrate that the CRD confers to PC5A and PACE4 properties to bind tissue inhibitors of metalloproteinases (TIMPs) and the cell surface. Confocal microscopy and biochemical analyses revealed that the CRD is essential for cell surface tethering of PC5A and PACE4 and that it colocalizes and coimmunoprecipitates with the full-length and C-terminal domain of TIMP-2. Surface-bound PC5A in TIMP-2 null fibroblasts was only observed upon coexpression with TIMP-2. In COS-1 cells, plasma membrane-associated PC5A can be displaced by heparin, suramin, or heparinases I and III and by competition with excess exogenous TIMP-2. Furthermore, PC5A and TIMP-2 are shown to be colocalized over the surface of enterocytes in the mouse duodenum and jejunum, as well as in liver sinusoids. In conclusion, the CRD of PC5A and PACE4 functions as a cell surface anchor favoring the processing of their cognate surface-anchored substrates, including endothelial lipase.
Role of Essential Genes in Mitochondrial Morphogenesis inSaccharomyces cerevisiae
Authors: Altmann Katrin , Westermann Benedikt
Published: September 2005

Mitochondria are essential organelles of eukaryotic cells. Inheritance and maintenance of mitochondrial structure depend on cytoskeleton-mediated organelle transport and continuous membrane fusion and fission events. However, in Saccharomyces cerevisiae most of the known components involved in these processes are encoded by genes that are not essential for viability. Here we asked which essential genes are required for mitochondrial distribution and morphology. To address this question, we performed a systematic screen of a yeast strain collection harboring essential genes under control of a regulatable promoter. This library contains 768 yeast mutants and covers approximately two thirds of all essential yeast genes. A total of 119 essential genes were found to be required for maintenance of mitochondrial morphology. Among these, genes were highly enriched that encode proteins involved in ergosterol biosynthesis, mitochondrial protein import, actin-dependent transport processes, vesicular trafficking, and ubiquitin/26S proteasome-dependent protein degradation. We conclude that these cellular pathways play an important role in mitochondrial morphogenesis and inheritance.
THE WELFARE EFFECTS OF DISTRIBUTION REGULATIONS IN OECD COUNTRIES
Authors: Bradford Scott
Published: August 2005

This article presents new data on distribution margins in eight OECD countries and uses an Applied General Equilibrium (AGE) framework to assess the welfare impacts of inefficient distribution. I estimate the extent to which regulations inflate margins. A comparison of margins across countries finds, in contrast to other studies, that Japan's margins are unusually high. The AGE simulations imply that inefficient distribution imposes substantial welfare costs, especially in Japan, with the costs rivaling those of trade barriers. The results also imply that distribution impediments can significantly reduce imports. (JEL D58, F13, L81)
The UNC-73/Trio RhoGEF-2 domain is required in separate isoforms for the regulation of pharynx pumping and normal neurotransmission in C. elegans
Authors: Steven Robert , Zhang Lijia , Culotti Joseph , Pawson Tony
Published: September 2005

In both Caenorhabditis elegans and Drosophila, UNC-73/Trio functions in axon guidance by signaling through the Rac GTPase to regulate cytoskeletal rearrangements necessary for growth cone migrations. Here, we show that the complex C. elegans unc-73 gene encodes at least eight differentially expressed UNC-73 intracellular protein isoforms. Previously reported mutations affecting UNC-73 isoforms encoding the Rac-specific RhoGEF-1 domain cause uncoordinated movement, correlating with defects in axon guidance. Mutations in isoforms encoding the Rho-specific RhoGEF-2 domain, which we describe here, result in L1 stage larval lethality with no associated axon guidance defects. Isoform-specific rescue experiments reveal separate functions for the various RhoGEF-2-containing UNC-73 isoforms, which would not likely be discovered by conventional genetic screening. UNC-73 D1 and D2 appear to function redundantly in pharynx muscle to regulate the rate and strength of pharynx pumping, and in the HSN neurons and vulval muscles to control egg laying. Isoforms C1, C2, E, and F act redundantly within the nervous system to regulate the speed of locomotion. The multiple UNC-73 isoforms containing Rac- and Rho-specific RhoGEF domains therefore have distinct physiological functions. In addition to its previously identified role involving RhoGEF-1 in migrating cells and growth cones, our data indicate that UNC-73 signals through RhoGEF-2 to regulate pharynx and vulva musculature and to modulate synaptic neurotransmission.
The cleavage of microphthalmia-associated transcription factor, MITF, by caspases plays an essential role in melanocyte and melanoma cell apoptosis
Authors: Larribere Lionel , Hilmi Caroline , Khaled Mehdi , Gaggioli Cédric , Bille Karine , Auberger Patrick , Ortonne Jean Paul , Ballotti Robert , Bertolotto Corine
Published: September 2005

Microphthalmia-associated transcription factor (MITF) M-form is a melanocyte-specific transcription factor that plays a key role in melanocyte development, survival, and differentiation. Here, we identified MITF as a new substrate of caspases and we characterized the cleavage site after Asp 345 in the C-terminal domain. We show that expression of a noncleavable form of MITF renders melanoma cells resistant to apoptotic stimuli, and we found that the C-terminal fragment generated upon caspase cleavage is endowed with a proapoptotic activity that sensitizes melanoma cells to death signals. The proapoptotic function gained by MITF following its processing by caspases provides a tissue-restricted means to modulate death in melanocyte and melanoma cells.
Identification of the scaramanga gene implicates Neuregulin3 in mammary gland specification
Authors: Howard Beatrice , Panchal Heena , McCarthy Afshan , Ashworth Alan
Published: September 2005

The mouse scaramanga (ska) mutation impairs mammary gland development such that both abrogation and stimulation of gland formation occurs. We used positional cloning to narrow the interval containing scaramanga (ska) to a 75.6-kb interval containing the distal part of the Neuregulin3 (Nrg3) gene. Within this region the only sequence difference between ska and wild-type mice is in a microsatellite repeat within intron 7. This alteration correlates with variations in Nrg3 expression profiles both at the whole embryo level and locally in the presumptive mammary region in ska mice. Localized expression of Nrg3 and its receptor, Erbb4, in the presumptive mammary region around the future bud site prior to morphological appearance of buds and the expression of bud epithelial markers further support an inductive role. Finally, Neuregulin3 (Nrg3)-soaked beads can induce expression of the early bud marker Lef1 in mouse embryo explant cultures, and epithelial bud formation can be observed histologically, suggesting that initiation of mammary bud development occurs. Taken together, these results indicate that a Neuregulin signaling pathway is involved in specification of mammary gland morphogenesis and support the long-held view that mesenchymal signal(s) are responsible for mammary gland inductive/initiating events.
Genetic interactions of separase regulatory subunits reveal the diverged Drosophila Cenp-C homolog
Authors: Heeger Sebastian , Leismann Oliver , Schittenhelm Ralf , Schraidt Oliver , Heidmann Stefan , Lehner Christian F.
Published: September 2005

Faithful transmission of genetic information during mitotic divisions depends on bipolar attachment of sister kinetochores to the mitotic spindle and on complete resolution of sister-chromatid cohesion immediately before the metaphase-to-anaphase transition. Separase is thought to be responsible for sister-chromatid separation, but its regulation is not completely understood. Therefore, we have screened for genetic loci that modify the aberrant phenotypes caused by overexpression of the regulatory separase complex subunits Pimples/securin and Three rows in Drosophila. An interacting gene was found to encode a constitutive centromere protein. Characterization of its centromere localization domain revealed the presence of a diverged CENPC motif. While direct evidence for an involvement of this Drosophila Cenp-C homolog in separase activation at centromeres could not be obtained, in vivo imaging clearly demonstrated that it is required for normal attachment of kinetochores to the spindle.
Fitting background-selection predictions to levels of nucleotide variation and divergence along the human autosomes
Authors: Reed Floyd A. , Akey Joshua M. , Aquadro Charles F.
Published: September 2005

The roles of positive directional selection (selective sweeps) and negative selection (background selection) in shaping the genome-wide distribution of genetic variation in humans remain largely unknown. Here, we optimize the parameter values of a model of the removal of deleterious mutations (background selection) to observed levels of human polymorphism, controlling for mutation rate heterogeneity by using interspecific divergence. A point of “best fit” was found between background-selection predictions and estimates of human effective population sizes, with reasonable parameter estimates whose uncertainty was assessed by bootstrapping. The results suggest that the purging of deleterious alleles has had some influence on shaping levels of human variation, although the effects may be subtle over the majority of the human genome. A significant relationship was found between background-selection predictions and measures of skew in the allele frequency distribution. The genome-wide action of selection (positive and/or negative) is required to explain this observation.
A microarray analysis of the rice transcriptome and its comparison to Arabidopsis
Authors: Ma Ligeng , Chen Chen , Liu Xigang , Jiao Yuling , Su Ning , Li Lin , Wang Xiangfeng , Cao Mengliang , Sun Ning , Zhang Xiuqing , Bao Jingyue , Li Jian , Pedersen Soren , Bolund Lars , Zhao Hongyu , Yuan Longping , Wong Gane Ka-Shu , Wang Jun , Deng Xing Wang , Wang Jian
Published: September 2005

Arabidopsis and rice are the only two model plants whose finished phase genome sequence has been completed. Here we report the construction of an oligomer microarray based on the presently known and predicted gene models in the rice genome. This microarray was used to analyze the transcriptional activity of the gene models in representative rice organ types. Expression of 86% of the 41,754 known and predicted gene models was detected. A significant fraction of these expressed gene models are organized into chromosomal regions, about 100 kb in length, that exhibit a coexpression pattern. Compared with similar genome-wide surveys of the Arabidopsis transcriptome, our results indicate that similar proportions of the two genomes are expressed in their corresponding organ types. A large percentage of the rice gene models that lack significant Arabidopsis homologs are expressed. Furthermore, the expression patterns of rice and Arabidopsis best-matched homologous genes in distinct functional groups indicate dramatic differences in their degree of conservation between the two species. Thus, this initial comparative analysis reveals some basic similarities and differences between the Arabidopsis and rice transcriptomes.
Independent intrachromosomal recombination events underlie the pericentric inversions of chimpanzee and gorilla chromosomes homologous to human chromosome 16
Authors: Goidts Violaine , Szamalek Justyna M. , de Jong Pieter J. , Cooper David N. , Chuzhanova Nadia , Hameister Horst , Kehrer-Sawatzki Hildegard
Published: September 2005

Analyses of chromosomal rearrangements that have occurred during the evolution of the hominoids can reveal much about the mutational mechanisms underlying primate chromosome evolution. We characterized the breakpoints of the pericentric inversion of chimpanzee chromosome 18 (PTR XVI), which is homologous to human chromosome 16 (HSA 16). A conserved 23-kb inverted repeat composed of satellites, LINE and Alu elements was identified near the breakpoints and could have mediated the inversion by bringing the chromosomal arms into close proximity with each other, thereby facilitating intrachromosomal recombination. The exact positions of the breakpoints may then have been determined by local DNA sequence homologies between the inversion breakpoints, including a 22-base pair direct repeat. The similarly located pericentric inversion of gorilla (GGO) chromosome XVI, was studied by FISH and PCR analysis. The p- and q-arm breakpoints of the inversions in PTR XVI and GGO XVI were found to occur at slightly different locations, consistent with their independent origin. Further, FISH studies of the homologous chromosomal regions in macaque and orangutan revealed that the region represented by HSA BAC RP11-696P19, which spans the inversion breakpoint on HSA 16q11-12, was derived from the ancestral primate chromosome homologous to HSA 1. After the divergence of orangutan from the other great apes ∼12 million years ago (Mya), a duplication of the corresponding region occurred followed by its interchromosomal transposition to the ancestral chromosome 16q. Thus, the most parsimonious interpretation is that the gorilla and chimpanzee homologs exhibit similar but nonidentical derived pericentric inversions, whereas HSA 16 represents the ancestral form among hominoids.
Evolutionary mechanisms shaping the genomic structure of the Williams-Beuren syndrome chromosomal region at human 7q11.23
Authors: Antonell Anna , de Luis Oscar , Domingo-Roura Xavier , Pérez-Jurado Luis Alberto
Published: September 2005

About 5% of the human genome consists of segmental duplications or low-copy repeats, which are large, highly homologous (>95%) fragments of sequence. It has been estimated that these segmental duplications emerged during the past ∼35 million years (Myr) of human evolution and that they correlate with chromosomal rearrangements. Williams-Beuren syndrome (WBS) is a segmental aneusomy syndrome that is the result of a frequent de novo deletion at 7q11.23, mediated by large (∼400-kb) region-specific complex segmental duplications composed of different blocks. We have precisely defined the structure of the segmental duplications on human 7q11.23 and characterized the copy number and structure of the orthologous regions in other primates (macaque, orangutan, gorilla, and chimpanzee). Our data indicate a recent origin and rapid evolution of the 7q11.23 segmental duplications, starting before the diversification of hominoids (∼12-16 million years ago [Mya]), with species-specific duplications and intrachromosomal rearrangements that lead to significant differences among those genomes. Alu sequences are located at most edges of the large hominoid-specific segmental duplications, suggesting that they might have facilitated evolutionary rearrangements. We propose a mechanistic model based on Alu-mediated duplicated transposition along with nonallelic homologous recombination for the generation and local expansion of the segmental duplications. The extraordinary rate of evolutionary turnover of this region, rich in segmental duplications, results in important genomic variation among hominoid species, which could be of functional relevance and predispose to disease.
The evolutionary fate of MULE-mediated duplications of host gene fragments in rice
Authors: Juretic Nikoleta , Hoen Douglas R. , Huynh Michael L. , Harrison Paul M. , Bureau Thomas E.
Published: September 2005

DNA transposons are known to frequently capture duplicated fragments of host genes. The evolutionary impact of this phenomenon depends on how frequently the fragments retain protein-coding function as opposed to becoming pseudogenes. Gene fragment duplication by Mutator-like elements (MULEs) has previously been documented in maize, Arabidopsis, and rice. Here we present a rigorous genome-wide analysis of MULEs in the model plant Oryza sativa (domesticated rice). We identify 8274 MULEs with intact termini and target-site duplications (TSDs) and show that 1337 of them contain duplicated host gene fragments. Through a detailed examination of the 5% of duplicated gene fragments that are transcribed, we demonstrate that virtually all cases contain pseudogenic features such as fragmented conserved protein domains, frameshifts, and premature stop codons. In addition, we show that the distribution of the ratio of nonsynonymous to synonymous amino acid substitution rates for the duplications agrees with the expected distribution for pseudogenes. We conclude that MULE-mediated host gene duplication results in the formation of pseudogenes, not novel functional protein-coding genes; however, the transcribed duplications possess characteristics consistent with a potential role in the regulation of host gene expression.
The Capacity for Thermal Protection of Photosynthetic Electron Transport Varies for Different Monoterpenes inQuercus ilex
Authors: Copolovici Lucian O. , Filella Iolanda , Llusià Joan , Niinemets Ülo , Peñuelas Josep
Published: August 2005

Heat stress resistance of foliar photosynthetic apparatus was investigated in the Mediterranean monoterpene-emitting evergreen sclerophyll species Quercus ilex. Leaf feeding with fosmidomycin, which is a specific inhibitor of the chloroplastic isoprenoid synthesis pathway, essentially stopped monoterpene emission and resulted in the decrease of the optimum temperature of photosynthetic electron transport from approximately 38°C to approximately 30°C. The heat stress resistance was partly restored by fumigation with 4 to 5 nmol mol−1 air concentrations of monoterpene α-pinene but not with fumigations with monoterpene alcohol α-terpineol. Analyses of monoterpene physicochemical characteristics demonstrated that α-pinene was primarily distributed to leaf gas and lipid phases, while α-terpineol was primarily distributed to leaf aqueous phase. Thus, for a common monoterpene uptake rate, α-terpineol is less efficient in stabilizing membrane liquid-crystalline structure and as an antioxidant in plant membranes. Furthermore, α-terpineol uptake rate (U) strongly decreased with increasing temperature, while the uptake rates of α-pinene increased with increasing temperature, providing a further explanation of the lower efficiency of thermal protection by α-terpineol. The temperature-dependent decrease of α-terpineol uptake was both due to decreases in stomatal conductance, gw, and increased volatility of α-terpineol at higher temperature that decreased the monoterpene diffusion gradient between the ambient air (FA) and leaf (FI; U = gw[FA − FI]). Model analyses suggested that α-pinene reacted within the leaf at higher temperatures, possibly within the lipid phase, thereby avoiding the decrease in diffusion gradient, FA − FI. Thus, these data contribute to the hypothesis of the antioxidative protection of leaf membranes during heat stress by monoterpenes. These data further suggest that fumigation with the relatively low atmospheric concentrations of monoterpenes that are occasionally observed during warm windless days in the Mediterranean canopies may significantly improve the heat tolerance of nonemitting vegetation that grows intermixed with emitting species.
Diurnal and Seasonal Variation of Isoprene Biosynthesis-Related Genes in Grey Poplar Leaves
Authors: Mayrhofer Sabine , Teuber Markus , Zimmer Ina , Louis Sandrine , Fischbach Robert J. , Schnitzler Jörg-Peter
Published: August 2005

Transcript levels of mRNA from 1-deoxy-d-xylulose 5-phosphate reductoisomerase (PcDXR), isoprene synthase (PcISPS), and phytoene synthase (PcPSY) showed strong seasonal variations in leaves of Grey poplar (Populus × canescens [Aiton] Sm.). These changes were dependent on the developmental stage and were strongly correlated to temperature and light. The expression rates of the genes PcDXR and PcISPS were found to be significantly correlated to each other, whereas the expression of the PcPSY gene showed a different seasonal pattern. Protein concentration and enzyme activity of PcISPS showed distinct seasonal patterns peaking in late summer, whereas highest transcription levels of PcISPS were observed in early summer. Moreover, correlation between PcISPS protein concentration and enzyme activity changed, in particular in autumn, when PcISPS protein levels remained high while enzyme activity declined, indicating posttranslational modifications of the enzyme. The positive correlation between dimethylallyl diphosphate levels and PcISPS protein content was found to be consistent with the demonstrated synchronized regulation of PcDXR and PcISPS, suggesting that metabolic flux through the 1-deoxy-d-xylulose 5-phosphate pathway and isoprene emission capacity are closely intercoordinated. Transcript levels of PcISPS showed strong diurnal variation with maximal values before midday in contrast to PcDXR, whose gene expression exhibited no clear intraday changes. During the course of a day, in vitro PcISPS activities did not change, whereas leaf dimethylallyl diphosphate levels and isoprene emission showed strong diurnal variations depending on actual temperature and light profiles on the respective day. These results illustrate that the regulation of isoprene biosynthesis in Grey poplar leaves seems to happen on transcriptional, posttranslational, and metabolic levels and is highly variable with respect to seasonal and diurnal changes in relation to temperature and light.
Mitochondria-Driven Changes in Leaf NAD Status Exert a Crucial Influence on the Control of Nitrate Assimilation and the Integration of Carbon and Nitrogen Metabolism
Authors: Dutilleul Christelle , Lelarge Caroline , Prioul Jean-Louis , De Paepe Rosine , Foyer Christine H. , Noctor Graham
Published: August 2005

The Nicotiana sylvestris mutant, CMS, lacks the mitochondrial gene nad7 and functional complex I, and respires using low-affinity NADH (alternative) mitochondrial dehydrogenases. Here, we show that this adjustment of respiratory pathways is associated with a profound modification of foliar carbon-nitrogen balance. CMS leaves are characterized by abundant amino acids compared to either wild-type plants or CMS in which complex I function has been restored by nuclear transformation with the nad7 cDNA. The metabolite profile of CMS leaves is enriched in amino acids with low carbon/nitrogen and depleted in starch and 2-oxoglutarate. Deficiency in 2-oxoglutarate occurred despite increased citrate and malate and higher capacity of key anaplerotic enzymes, notably the mitochondrial NAD-dependent isocitrate dehydrogenase. The accumulation of nitrogen-rich amino acids was not accompanied by increased expression of enzymes involved in nitrogen assimilation. Partitioning of 15N-nitrate into soluble amines was enhanced in CMS leaf discs compared to wild-type discs, especially in the dark. Analysis of pyridine nucleotides showed that both NAD and NADH were increased by 2-fold in CMS leaves. The growth retardation of CMS relative to the wild type was highly dependent on photoperiod, but at all photoperiod regimes the link between high contents of amino acids and NADH was observed. Together, the data provide strong evidence that (1) NADH availability is a critical factor in influencing the rate of nitrate assimilation and that (2) NAD status plays a crucial role in coordinating ammonia assimilation with the anaplerotic production of carbon skeletons.
Secretome Analysis Reveals anArabidopsisLipase Involved in Defense againstAlternaria brassicicola
Authors: Oh Il Seok , Park Ae Ran , Bae Min Seok , Kwon Sun Jae , Kim Young Soon , Lee Ji Eun , Kang Na Young , Lee Sumin , Cheong Hyeonsook , Park Ohkmae K.
Published: August 2005

The Arabidopsis thaliana secretome was analyzed by the proteomic approach, which led to the identification of secreted proteins implicated in many aspects of cell biology. We then investigated the change in the Arabidopsis secretome in response to salicylic acid and identified several proteins involved in pathogen response. One of these, a secreted lipase with a GDSL-like motif designated GDSL LIPASE1 (GLIP1), was further characterized for its function in disease resistance. glip1 plants were markedly more susceptible to infection by the necrotrophic fungus Alternaria brassicicola compared with the parental wild-type plants. The recombinant GLIP1 protein possessed lipase and antimicrobial activities that directly disrupt fungal spore integrity. Furthermore, GLIP1 appeared to trigger systemic resistance signaling in plants when challenged with A. brassicicola, because pretreatment of the glip1 mutant with recombinant GLIP1 protein inhibited A. brassicicola–induced cell death in both peripheral and distal leaves. Moreover, glip1 showed altered expression of defense- and ethylene-related genes. GLIP1 transcription was increased by ethephon, the ethylene releaser, but not by salicylic acid or jasmonic acid. These results suggest that GLIP1, in association with ethylene signaling, may be a critical component in plant resistance to A. brassicicola.
Why link personal research and teaching?
Authors: Berman Brown Reva
Published: September 2005

Purpose

The purpose of this paper is to highlight issues concerning the linking of research to teaching.

Design/methodology/approach

The paper engages with two assumptions which appear to be taken for granted: there should be an overt and strong link between one's own research and one's teaching; and one's active involvement in the research process should, at the very least, underpin, the quality of one's teaching, and at best, improve it.

Findings

There is a link between research and teaching (though the strength of the link is problematic). The link is not only a matter of intellectual or disciplinary import, but is complicated by political and vested interests. The two extremes of research and teaching can be bridged by scholarship or learning, or both together. It is unnecessary and counter‐productive to demand of academics that they should be simultaneously good researchers and good teachers, although this requirement is unlikely to be realised in practice. There is no obligation whatever for academics to overtly link their own personal research to their teaching in order to be considered good teachers.

Originality/value

The paper queries both these assumptions which appear to be influencing how policy concerning research and teaching is dealt with in higher education institutions, and investigates the implications of feeling obliged to teach students using personal research.