bluuebunny/crossref_metadata_2025 huggingface dataset:
Metal trafficking for nitrogen fixation: NifQ donates molybdenum to NifEN/NifH for the biosynthesis of the nitrogenase FeMo-cofactor
Authors: Hernandez Jose A. , Curatti Leonardo , Aznar Constantino P. , Perova Zinaida , Britt R. David , Rubio Luis M.
Published: August 2008

The molybdenum nitrogenase, present in a diverse group of bacteria and archea, is the major contributor to biological nitrogen fixation. The nitrogenase active site contains an iron–molybdenum cofactor (FeMo-co) composed of 7Fe, 9S, 1Mo, one unidentified light atom, and homocitrate. The
nifQ
gene was known to be involved in the incorporation of molybdenum into nitrogenase. Here we show direct biochemical evidence for the role of NifQ in FeMo-co biosynthesis. As-isolated NifQ was found to carry a molybdenum–iron–sulfur cluster that serves as a specific molybdenum donor for FeMo-co biosynthesis. Purified NifQ supported
in vitro
FeMo-co synthesis in the absence of an additional molybdenum source. The mobilization of molybdenum from NifQ required the simultaneous participation of NifH and NifEN in the
in vitro
FeMo-co synthesis assay, suggesting that NifQ would be the physiological molybdenum donor to a hypothetical NifEN/NifH complex.
A key developmental regulator controls the synthesis of the antibiotic erythromycin in
Saccharopolyspora erythraea
Authors: Chng Chinping , Lum Amy M. , Vroom Jonathan A. , Kao Camilla M.
Published: August 2008

Saccharopolyspora erythraea
makes erythromycin, an antibiotic commonly used in human medicine. Unusually, the erythromycin biosynthetic (
ery
) cluster lacks a pathway-specific regulatory gene. We isolated a transcriptional regulator of the
ery
biosynthetic genes from
S. erythraea
and found that this protein appears to directly link morphological changes caused by impending starvation to the synthesis of a molecule that kills other bacteria, i.e., erythromycin. DNA binding assays, liquid and affinity chromatography, MALDI-MS analysis, and
de novo
sequencing identified this protein (
M
r
= 18 kDa) as the
S. erythraea
ortholog of BldD, a key regulator of development in
Streptomyces coelicolor
. Recombinant
S. erythraea
BldD bound to all five regions containing promoters in the
ery
cluster as well as to its own promoter, the latter with an order-of-magnitude stronger than to the
ery
promoters. Deletion of
bldD
in
S. erythraea
decreased the erythromycin titer in a liquid culture 7-fold and blocked differentiation on a solid medium. Moreover, an industrial strain of
S. erythraea
with a higher titer of erythromycin expressed more BldD than a wild-type strain during erythromycin synthesis. Together, these results suggest that BldD concurrently regulates the synthesis of erythromycin and morphological differentiation. The
ery
genes are the first direct targets of a BldD ortholog to be identified that are positively regulated.
Crowded, cell-like environment induces shape changes in aspherical protein
Authors: Homouz Dirar , Perham Michael , Samiotakis Antonios , Cheung Margaret S. , Wittung-Stafshede Pernilla
Published: August 2008

How the crowded environment inside cells affects the structures of proteins with aspherical shapes is a vital question because many proteins and protein–protein complexes
in vivo
adopt anisotropic shapes. Here we address this question by combining computational and experimental studies of a football-shaped protein (i.e.,
Borrelia burgdorferi
VlsE) in crowded, cell-like conditions. The results show that macromolecular crowding affects protein-folding dynamics as well as overall protein shape. In crowded milieus, distinct conformational changes in VlsE are accompanied by secondary structure alterations that lead to exposure of a hidden antigenic region. Our work demonstrates the malleability of “native” proteins and implies that crowding-induced shape changes may be important for protein function and malfunction
in vivo
.
Experimental approaches to kinetics of gas diffusion in hydrogenase
Authors: Leroux Fanny , Dementin Sébastien , Burlat Bénédicte , Cournac Laurent , Volbeda Anne , Champ Stéphanie , Martin Lydie , Guigliarelli Bruno , Bertrand Patrick , Fontecilla-Camps Juan , Rousset Marc , Léger Christophe
Published: August 2008

Hydrogenases, which catalyze H
2
to H
+
conversion as part of the bioenergetic metabolism of many microorganisms, are among the metalloenzymes for which a gas-substrate tunnel has been described by using crystallography and molecular dynamics. However, the correlation between protein structure and gas-diffusion kinetics is unexplored. Here, we introduce two quantitative methods for probing the rates of diffusion within hydrogenases. One uses protein film voltammetry to resolve the kinetics of binding and release of the competitive inhibitor CO; the other is based on interpreting the yield in the isotope exchange assay. We study structurally characterized mutants of a NiFe hydrogenase, and we show that two mutations, which significantly narrow the tunnel near the entrance of the catalytic center, decrease the rates of diffusion of CO and H
2
toward and from the active site by up to 2 orders of magnitude. This proves the existence of a functional channel, which matches the hydrophobic cavity found in the crystal. However, the changes in diffusion rates do not fully correlate with the obstruction induced by the mutation and deduced from the x-ray structures. Our results demonstrate the necessity of measuring diffusion rates and emphasize the role of side-chain dynamics in determining these.
Fluid helium at conditions of giant planetary interiors
Authors: Stixrude Lars , Jeanloz Raymond
Published: August 2008

As the second most-abundant chemical element in the universe, helium makes up a large fraction of giant gaseous planets, including Jupiter, Saturn, and most extrasolar planets discovered to date. Using first-principles molecular dynamics simulations, we find that fluid helium undergoes temperature-induced metallization at high pressures. The electronic energy gap (band gap) closes at 20,000 K at a density half that of zero-temperature metallization, resulting in electrical conductivities greater than the minimum metallic value. Gap closure is achieved by a broadening of the valence band via increased
s–p
hydridization with increasing temperature, and this influences the equation of state: The Grüneisen parameter, which determines the adiabatic temperature–depth gradient inside a planet, changes only modestly, decreasing with compression up to the high-temperature metallization and then increasing upon further compression. The change in electronic structure of He at elevated pressures and temperatures has important implications for the miscibility of helium in hydrogen and for understanding the thermal histories of giant planets.
Expression of Globo H and SSEA3 in breast cancer stem cells and the involvement of fucosyl transferases 1 and 2 in Globo H synthesis
Authors: Chang Wen-Wei , Lee Chien Hsin , Lee Peishan , Lin Juway , Hsu Chun-Wei , Hung Jung-Tung , Lin Jin-Jin , Yu Jyh-Cherng , Shao Li-en , Yu John , Wong Chi-Huey , Yu Alice L.
Published: August 2008

We examined the expression in breast cancer stem cells (BCSCs) of Globo H, a potential tumor-associated antigen for immunotherapy of epithelial cancers including breast cancer. Flow cytometry revealed Globo H expression in 25/41 breast cancer specimens (61.0%). Non-BCSCs from 25/25 and BCSCs from 8/40 (20%) expressed Globo H. We showed the expression of stage-specific embryonic antigen 3 (SSEA3), the pentasaccharide precursor of Globo H, in 31/40 (77.5%) tumors. Non-BCSCs from 29/31 and BCSCs from 25/40 (62.5%) expressed SSEA3. Like Globo H, SSEA3 expression in normal tissues was predominately at the secretory borders of epithelium, where access to the immune system is restricted. Immunization of mice with Globo H-KLH and α-GalCer induced antibodies reactive with Globo H and SSEA3, suggesting that a Globo H-based vaccine will target tumor cells expressing Globo H or SSEA3. We next sought to reduce Globo H expression by siRNA targeting fucosyltransferase (
FUT
) 1 and 2, which mediate alpha-1,2 linkage of fucose to SSEA3 to generate Globo H. We showed both genes to be involved in the biosynthesis of Globo H. Moreover,
FUT2
expression in BCSCs was significantly lower than in non-BCSCs harvested from a primary human breast cancer in NOD/SCID mouse, whereas
FUT1
was slightly lower in BCSCs. Thus, the lower expression of Globo H in BCSCs may be attributed to less FUT2/FUT1, and to reduced SSEA3 in BCSCs compared with non-BCSCs. Our findings provide insight into further development of a Globo H-based vaccine and
FUT1/FUT2
-targeted therapy for breast cancer.
Tempol-mediated activation of latent iron regulatory protein activity prevents symptoms of neurodegenerative disease in IRP2 knockout mice
Authors: Ghosh Manik C. , Tong Wing-Hang , Zhang Deliang , Ollivierre-Wilson Hayden , Singh Anamika , Krishna Murali C. , Mitchell James B. , Rouault Tracey A.
Published: August 2008

In mammals, two homologous cytosolic regulatory proteins, iron regulatory protein 1 (also known as IRP1 and Aco1) and iron regulatory protein 2 (also known as IRP2 and Ireb2), sense cytosolic iron levels and posttranscriptionally regulate iron metabolism genes, including transferrin receptor 1 (TfR1) and ferritin H and L subunits, by binding to iron-responsive elements (IREs) within target transcripts. Mice that lack IRP2 develop microcytic anemia and neurodegeneration associated with functional cellular iron depletion caused by low TfR1 and high ferritin expression. IRP1 knockout (IRP1
−/−
) animals do not significantly misregulate iron metabolism, partly because IRP1 is an iron-sulfur protein that functions mainly as a cytosolic aconitase in mammalian tissues and IRP2 activity increases to compensate for loss of the IRE binding form of IRP1. The neurodegenerative disease of IRP2
−/−
animals progresses slowly as the animals age. In this study, we fed IRP2
−/−
mice a diet supplemented with a stable nitroxide, Tempol, and showed that the progression of neuromuscular impairment was markedly attenuated. In cell lines derived from IRP2
−/−
animals, and in the cerebellum, brainstem, and forebrain of animals maintained on the Tempol diet, IRP1 was converted from a cytosolic aconitase to an IRE binding protein that stabilized the TfR1 transcript and repressed ferritin synthesis. We suggest that Tempol protected IRP2
−/−
mice by disassembling the cytosolic iron-sulfur cluster of IRP1 and activating IRE binding activity, which stabilized the TfR1 transcript, repressed ferritin synthesis, and partially restored normal cellular iron homeostasis in the brain.
Dual regulation of
NR2B
and
NR2C
expression by NMDA receptor activation in mouse cerebellar granule cell cultures
Authors: Iijima Kouichirou , Abe Haruka , Okazawa Makoto , Moriyoshi Koki , Nakanishi Shigetada
Published: August 2008

In the developing cerebellum, switching of the subunit composition of NMDA receptors occurs in granule cells from NR2B-containing receptors to NR2C-containing ones. We investigated the mechanisms underlying switching of NR2B and NR2C subunit composition in primary cultures of mouse granule cells at the physiological KCl concentration (5 mM). Granule cells extensively extended their neuritic processes 48 h after having been cultured in serum-free medium containing 5 mM KCl. Consistent with this morphological change, NR2B mRNA and NR2C mRNA were down- and up-regulated, respectively, in the granule cells. This dual regulation of the two mRNAs was abrogated by blocking excitation of granule cells with TTX. This neuronal activity–dependent regulation of NR2B and NR2C mRNAs was abolished by the addition of selective antagonists of AMPA receptors and NMDA receptors. Furthermore, the dual regulation of NR2B and NR2C mRNAs in TTX-treated cells was restored by the addition of NMDA in the presence of the AMPA receptor antagonist, but not by that of AMPA in the presence of the NMDA receptor antagonist. Importantly, the NMDA receptor activation drove the NR2B/NR2C switching of NMDA receptors in the cell-surface membrane of granule cells. This investigation demonstrates that stimulation of NMDA receptors in conjunction with the AMPA receptor–mediated excitation of granule cells plays a key role in functional subunit switching of NMDA receptors in maturing granule cells at the physiological KCl concentration.
The functional basis of face evaluation
Authors: Oosterhof Nikolaas N. , Todorov Alexander
Published: August 2008

People automatically evaluate faces on multiple trait dimensions, and these evaluations predict important social outcomes, ranging from electoral success to sentencing decisions. Based on behavioral studies and computer modeling, we develop a 2D model of face evaluation. First, using a principal components analysis of trait judgments of emotionally neutral faces, we identify two orthogonal dimensions, valence and dominance, that are sufficient to describe face evaluation and show that these dimensions can be approximated by judgments of trustworthiness and dominance. Second, using a data-driven statistical model for face representation, we build and validate models for representing face trustworthiness and face dominance. Third, using these models, we show that, whereas valence evaluation is more sensitive to features resembling expressions signaling whether the person should be avoided or approached, dominance evaluation is more sensitive to features signaling physical strength/weakness. Fourth, we show that important social judgments, such as threat, can be reproduced as a function of the two orthogonal dimensions of valence and dominance. The findings suggest that face evaluation involves an overgeneralization of adaptive mechanisms for inferring harmful intentions and the ability to cause harm and can account for rapid, yet not necessarily accurate, judgments from faces.
The structure of HLA-DR52c: Comparison to other HLA-DRB3 alleles
Authors: Dai Shaodong , Crawford Frances , Marrack Philippa , Kappler John W.
Published: August 2008

Class II major histocompatibility complex (MHCII) molecules present antigens to CD4+T cells. In addition to the most commonly studied human MHCII isotype, HLA-DR, whose β chain is encoded by the HLA-DRB1 locus, several other isotypes that use the same α chain but have β chains encoded by other genes. These other DR molecules also are expressed in antigen-presenting cells and are known to participate in peptide presentation to T cells and to be recognized as alloantigens by other T cells. Like some of the HLA-DRB1 alleles, several of these alternate DR molecules have been associated with specific autoimmune diseases and T cell hypersensitivity. Here we present the structure of an HLA-DR molecule (DR52c) containing one of these alternate β chains (HLA-DRB3*0301) bound to a self-peptide derived from the Tu elongation factor. The molecule shares structurally conserved elements with other MHC class II molecules but has some unique features in the peptide-binding groove. Comparison of the three major HLA-DBR3 alleles (DR52a, b, and c) suggests that they were derived from one another by recombination events that scrambled the four major peptide-binding pockets at peptide positions 1, 4, 6, and 9 but left virtually no polymorphisms elsewhere in the molecules.
Short Article: Superior Discrimination between Similar Stimuli after Simultaneous Exposure
Authors: Mundy Matthew E. , Honey Robert C. , Dwyer Dominic M.
Published: August 2008

Human participants received unsupervised exposure to difficult-to-discriminate chequerboard stimuli (e.g., AX and BX), before learning a discrimination between them. Experiment 1 demonstrated that prior exposure enhanced later discrimination and that intermixed exposure (AX, BX, AX, BX …) resulted in better subsequent discrimination than did blocked exposure (CY, CY … DY, DY …). Experiment 2 showed that simultaneous exposure to two similar stimuli (AX–BX, BX–AX …) facilitated the later acquisition of a successive discrimination, more than successive exposure (AX–AX, BX–BX …). These results parallel those observed by Mundy, Honey, and Dwyer (2007) who used pictures of human faces as stimuli and establish the generality of the fact that simultaneous exposure produces a particularly marked perceptual learning effect.
Poloidal field amplification in a coaxial compact toroid accelerator
Authors: Horton R.D. , Hwang D.Q. , Howard S. , Brockington S.J. , Evans R.W.
Published: August 2008

The Compact Toroid Injection Experiment (CTIX) produces spheromak-like compact toroids (SCTs) without external power switching, initiating a discharge by pulsed gas injection into a formation region containing a seed magnetic field generated by a solenoidal coil. After formation, the plasma is driven by an inductively delayed capacitor bank into an acceleration region, where surface axial and toroidal magnetic fields are measured at several axial positions. Due to strong eddy-current effects, formation-region magnetic field cannot be simply computed; instead, it is measured using the response of axial and radial test coils in the formation region to short solenoid test current pulses. A temporal and spatial reconstruction method is developed allowing formation-region field to be computed from the test-coil data for any CTIX discharge of identical solenoid geometry. By varying the peak value and timing of solenoidal current, curves of peak accelerator-region field as a function of initial formation-region field are developed. Curves of peak accelerator-region axial magnetic field are thereby found to be highly nonlinear functions of formation-region field, showing a threshold value for the formation-region field of approximately 5 G, above which acceleration-region field saturates at values between 2 and 12 kG. The direction of acceleration-region axial field reverses sign when the direction of solenoid current is reversed. Saturated accelerator-region axial field is a function of axial position and accelerator voltage, and is typically comparable to toroidal field at the same location. The ratio of accelerator-region to formation-region axial field commonly exceeds 1000 near the onset of saturation. This large amplification is of practical advantage for delayed plasma breakdown on CTIX, allowing a modest seed field to produce high poloidal fields, which are necessary for intense SCT acceleration. The results may also provide a useful benchmark for numerical simulation of the conversion of abundant toroidal field into poloidal field in a plasma with comparatively low dissipation.
Filamentary current structures in the Madison Symmetric Torus
Authors: Piovesan P. , Almagri A. , Chapman B.E. , Craig D. , Marrelli L. , Martin P. , Prager S.C. , Sarff J.S.
Published: August 2008

Filamentary structures are observed during edge relaxation events associated with spontaneous enhanced confinement periods in the Madison Symmetric Torus reversed-field pinch (Dexter R.N., Kerst D.W., Lovell T.W., Prager S.C. and Sprott J.C. 1991 Fusion Technol.
19 131). The spatiotemporal shape of these structures is measured through extended toroidal and poloidal arrays of high-frequency magnetic probes at the plasma boundary. A simple model is used to interpret these structures as field-aligned current filaments, which are born at the reversal surface and propagate in the toroidal direction. The results found in MST share interesting commonalities with recent observations of filaments made during edge-localized modes in tokamaks and spherical tokamaks, as far as typical time scales, spatial localization and particle transport are concerned. Moreover, the dynamo effect produced by these events is estimated and compared with that produced during sawteeth. Though a single event has a small impact, the cumulative contribution of many of them produces a significant dynamo effect.
Screening of the resistive-wall impedance by a cylindrical electron plasma
Authors: Al-Khateeb A , Hasse R W , Boine-Frankenheim O , Hofmann I
Published: August 2008

The effect of an electron cloud on the longitudinal coupling impedance is studied by idealizing it as a cold and uniformly distributed non-neutral plasma of electrons. The beam pipe is assumed to be of circular cross section with a thick resistive wall and the beam charge is idealized as a uniform disk. The electron contribution to the charge and current densities is obtained from the collective electron response to the beam passage through the pipe. In the presence of the electron background, a general closed formula for the longitudinal coupling impedance is obtained. The screening of the coupling impedance with the density of the electron plasma is studied and discussed for typical parameters in an accelerator beam pipe for the under-dense and the over-dense plasma regions.
Efg1-mediated Recruitment of NuA4 to Promoters Is Required for Hypha-specific Swi/Snf Binding and Activation inCandida albicans
Authors: Lu Yang , Su Chang , Mao Xuming , Raniga Prashna Pala , Liu Haoping , Chen Jiangye
Published: August 2008

Efg1 is essential for hyphal development and virulence in the human pathogenic fungus Candida albicans. How Efg1 regulates gene expression is unknown. Here, we show that Efg1 interacts with components of the nucleosome acetyltransferase of H4 (NuA4) histone acetyltransferase (HAT) complex in both yeast and hyphal cells. Deleting YNG2, a subunit of the NuA4 HAT module, results in a significant decrease in the acetylation level of nucleosomal H4 and a profound defect in hyphal development, as well as a defect in the expression of hypha-specific genes. Using chromatin immunoprecipitation, Efg1 and the NuA4 complex are found at the UAS regions of hypha-specific genes in both yeast and hyphal cells, and Efg1 is required for the recruitment of NuA4. Nucleosomal H4 acetylation at the promoters peaks during initial hyphal induction in an Efg1-dependent manner. We also find that Efg1 bound to the promoters of hypha-specific genes is critical for recruitment of the Swi/Snf chromatin remodeling complex during hyphal induction. Our data show that the recruitment of the NuA4 complex by Efg1 to the promoters of hypha-specific genes is required for nucleosomal H4 acetylation at the promoters during hyphal induction and for subsequent binding of Swi/Snf and transcriptional activation.
Arf GTPase-activating Protein ASAP1 Interacts with Rab11 Effector FIP3 and Regulates Pericentrosomal Localization of Transferrin Receptor–positive Recycling Endosome
Authors: Inoue Hiroki , Ha Vi Luan , Prekeris Rytis , Randazzo Paul A.
Published: August 2008

ADP-ribosylation factors (Arfs) and Arf GTPase-activating proteins (GAPs) are key regulators of membrane trafficking and the actin cytoskeleton. The Arf GAP ASAP1 contains an N-terminal BAR domain, which can induce membrane tubulation. Here, we report that the BAR domain of ASAP1 can also function as a protein binding site. Two-hybrid screening identified FIP3, which is a putative Arf6- and Rab11-effector, as a candidate ASAP1 BAR domain-binding protein. Both coimmunoprecipitation and in vitro pulldown assays confirmed that ASAP1 directly binds to FIP3 through its BAR domain. ASAP1 formed a ternary complex with Rab11 through FIP3. FIP3 binding to the BAR domain stimulated ASAP1 GAP activity against Arf1, but not Arf6. ASAP1 colocalized with FIP3 in the pericentrosomal endocytic recycling compartment. Depletion of ASAP1 or FIP3 by small interfering RNA changed the localization of transferrin receptor, which is a marker of the recycling endosome, in HeLa cells. The depletion also altered the trafficking of endocytosed transferrin. These results support the conclusion that ASAP1, like FIP3, functions as a component of the endocytic recycling compartment.
Spatiotemporal Analysis of Differential Akt Regulation in Plasma Membrane Microdomains
Authors: Gao Xinxin , Zhang Jin
Published: August 2008

As a central kinase in the phosphatidylinositol 3-kinase pathway, Akt has been the subject of extensive research; yet, spatiotemporal regulation of Akt in different membrane microdomains remains largely unknown. To examine dynamic Akt activity in membrane microdomains in living cells, we developed a specific and sensitive fluorescence resonance energy transfer-based Akt activity reporter, AktAR, through systematic testing of different substrates and fluorescent proteins. Targeted AktAR reported higher Akt activity with faster activation kinetics within lipid rafts compared with nonraft regions of plasma membrane. Disruption of rafts attenuated platelet-derived growth factor (PDGF)-stimulated Akt activity in rafts without affecting that in nonraft regions. However, in insulin-like growth factor-1 (IGF)-1 stimulation, Akt signaling in nonraft regions is dependent on that in raft regions. As a result, cholesterol depletion diminishes Akt activity in both regions. Thus, Akt activities are differentially regulated in different membrane microdomains, and the overall activity of this oncogenic pathway is dependent on raft function. Given the increased abundance of lipid rafts in some cancer cells, the distinct Akt-activating characteristics of PDGF and IGF-1, in terms of both effectiveness and raft dependence, demonstrate the capabilities of different growth factor signaling pathways to transduce differential oncogenic signals across plasma membrane.
Frequency and fate of microRNA editing in human brain
Authors: Kawahara Yukio , Megraw Molly , Kreider Edward , Iizasa Hisashi , Valente Louis , Hatzigeorgiou Artemis G. , Nishikura Kazuko
Published: August 2008

Primary transcripts of certain microRNA (miRNA) genes (pri-miRNAs) are subject to RNA editing that converts adenosine to inosine (A→I RNA editing). However, the frequency of the pri-miRNA editing and the fate of edited pri-miRNAs remain largely to be determined. Examination of already known pri-miRNA editing sites indicated that adenosine residues of the UAG triplet sequence might be edited more frequently. In the present study, therefore, we conducted a large-scale survey of human pri-miRNAs containing the UAG triplet sequence. By direct sequencing of RT-PCR products corresponding to pri-miRNAs, we examined 209 pri-miRNAs and identified 43 UAG and also 43 non-UAG editing sites in 47 pri-miRNAs, which were highly edited in human brain. In vitro miRNA processing assay using recombinant Drosha-DGCR8 and Dicer-TRBP (the human immuno deficiency virus transactivating response RNA-binding protein) complexes revealed that a majority of pri-miRNA editing is likely to interfere with the miRNA processing steps. In addition, four new edited miRNAs with altered seed sequences were identified by targeted cloning and sequencing of the miRNAs that would be processed from edited pri-miRNAs. Our studies predict that ∼16% of human pri-miRNAs are subject to A→I editing and, thus, miRNA editing could have a large impact on the miRNA-mediated gene silencing.
Genome-wide identification ofin vivoprotein-DNA binding sites from ChIP-Seq data
Authors: Jothi Raja , Cuddapah Suresh , Barski Artem , Cui Kairong , Zhao Keji
Published: August 2008

ChIP-Seq, which combines chromatin immunoprecipitation (ChIP) with ultra high-throughput massively parallel sequencing, is increasingly being used for mapping protein–DNA interactions in-vivo on a genome scale. Typically, short sequence reads from ChIP-Seq are mapped to a reference genome for further analysis. Although genomic regions enriched with mapped reads could be inferred as approximate binding regions, short read lengths (∼25-50nt) pose challenges for determining the exact binding sites within these regions. Here, we present SISSRs (Site Identification from Short Sequence Reads), a novel algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments. The sensitivity and specificity of SISSRs are demonstrated by applying it on ChIP-Seq data for three widely studied and well-characterized human transcription factors: CTCF (CCCTC-binding factor), NRSF (neuron-restrictive silencer factor) and STAT1 (signal transducer and activator of transcription protein 1). We identified 26814, 5813 and 73956 binding sites for CTCF, NRSF and STAT1 proteins, respectively, which is 32, 299 and 78% more than that inferred previously for the respective proteins. Motif analysis revealed that an overwhelming majority of the identified binding sites contained the previously established consensus binding sequence for the respective proteins, thus attesting for SISSRs’ accuracy. SISSRs’ sensitivity and precision facilitated further analyses of ChIP-Seq data revealing interesting insights, which we believe will serve as guidance for designing ChIP-Seq experiments to map in vivo protein–DNA interactions. We also show that tag densities at the binding sites are a good indicator of protein–DNA binding affinity, which could be used to distinguish and characterize strong and weak binding sites. Using tag density as an indicator of DNA-binding affinity, we have identified core residues within the NRSF and CTCF binding sites that are critical for a stronger DNA binding.
The RecU Holliday junction resolvase acts at early stages of homologous recombination
Authors: Cañas Cristina , Carrasco Begoña , Ayora Silvia , Alonso Juan C.
Published: August 2008

Homologous recombination is essential for DNA repair and generation of genetic diversity in all organisms. It occurs through a series of presynaptic steps where the substrate is presented to the recombinase (RecA in bacteria). Then, the recombinase nucleoprotein filament mediates synapsis by first promoting the formation of a D-loop and later of a Holliday junction (HJ) that is subsequently cleaved by the HJ resolvase. The coordination of the synaptic step with the late resolution step is poorly understood. Bacillus subtilis RecU catalyzes resolution of HJs, and biochemical evidence suggests that it might modulate RecA. We report here the isolation and characterization of two mutants of RecU (recU56 and recU71), which promote resolution of HJs, but do not promote RecA modulation. In vitro, the RecU mutant proteins (RecUK56A or RecUR71A) bind and cleave HJs and interact with RuvB. RecU interacts with RecA and inhibits its single-stranded DNA-dependent dATP hydrolysis, but RecUK56A and RecUR71A do not exert a negative effect on the RecA dATPase and fail to interact with it. Both activities are important in vivo since RecU mutants impaired only in RecA interaction are as sensitive to DNA damaging agents as a deletion mutant.
Tetrahymena thermophila and Candida albicans Group I intron-derived ribozymes can catalyze the trans-excision-splicing reaction
Authors: Dotson P. Patrick , Johnson Ashley K. , Testa Stephen M.
Published: August 2008

Group I intron-derived ribozymes can catalyze a variety of non-native reactions. For the trans-excision-splicing (TES) reaction, an intron-derived ribozyme from the opportunistic pathogen Pneumocystis carinii catalyzes the excision of a predefined region from within an RNA substrate with subsequent ligation of the flanking regions. To establish TES as a general ribozyme-mediated reaction, intron-derived ribozymes from Tetrahymena thermophila and Candida albicans, which are similar to but not the same as that from Pneumocystis, were investigated for their propensity to catalyze the TES reaction. We now report that the Tetrahymena and Candida ribozymes can catalyze the excision of a single nucleotide from within their ribozyme-specific substrates. Under the conditions studied, the Tetrahymena and Candida ribozymes, however, catalyze the TES reaction with lower yields and rates [Tetrahymena(kobs) = 0.14/min and Candida (kobs) = 0.34/min] than the Pneumocystis ribozyme (kobs = 3.2/min). The lower yields are likely partially due to the fact that the Tetrahymena and Candida catalyze additional reactions, separate from TES. The differences in rates are likely partially due to the individual ribozymes ability to effectively bind their 3’ terminal guanosines as intramolecular nucleophiles. Nevertheless, our results demonstrate that group I intron-derived ribozymes are inherently able to catalyze the TES reaction.
Leptosphaeria maculans Elicits Apoptosis Coincident with Leaf Lesion Formation and Hyphal Advance in Brassica napus
Authors: Li Caixia , Barker Susan J. , Gilchrist David G. , Lincoln James E. , Cowling Wallace A.
Published: August 2008

Programmed cell death, with many of the morphological markers of apoptosis, is increasingly recognized as an important process in plant disease. We have investigated the involvement and potential role of apoptosis during the formation of leaf lesions by the fungus Leptosphaeria maculans on susceptible Brassica napus cv. Westar. There were no signs of host cell damage until 7 to 8 days postinoculation (dpi), when trypan-blue-stained leaf mesophyll cells were first detected. Hyphae were visible in the intercellular spaces of the inoculated area from 5 dpi and were associated with trypan-blue-stained cells at 8 to 9 dpi. Hallmarks of apoptosis, observed coincident with or immediately prior to the formation of leaf lesions at 8 to 10 dpi, included membrane shrinkage of the mesophyll cell cytoplasm, loss of cell to cell contact in mesophyll cells, and terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling of nuclei in apparently “healthy” tissue immediately adjacent to dead areas. Hyphae were highly branched and prolific in the “healthy” tissue immediately adjacent to dead areas 9 to 10 dpi, and formed pycnidia inside dead areas 11 to 12 dpi. Coinfiltration of the tetrapeptide caspase inhibitor Ac-DEVD-CHO with spores of the pathogen significantly suppressed development of leaf lesions but did not affect fungus viability. We hypothesize that L. maculans elicits apoptosis as a dependent component of pathogenesis in susceptible B. napus, and that the fungus uses apoptotic cells as a source of nutrition for reproduction and further growth.
Frictionless multiple impacts in multibody systems. I. Theoretical framework
Authors: Liu Caishan , Zhao Zhen , Brogliato Bernard
Published: August 2008

A new method is proposed that can deal with multi-impact problems and produce energetically consistent and unique post-impact velocities. A distributing law related to the energy dispersion is discovered by mapping the time scale into the impulsive scale for bodies composed of rate-independent materials. It indicates that the evolution of the kinetic energy during the impacts is closely associated with therelative contact stiffnessand therelative potential energystored at the contact points. This distributing law is combined with the Darboux–Keller method of taking the normal impulse as an independent ‘time-like’ variable, which obeys a guideline for the selection of an independent normal impulse. Local energy losses are modelled with energetic coefficients of restitution at each contact point. Theoretical developments are presented in the first part in this paper. The second part is dedicated to numerical simulations where numerous and accurate results prove the validity of the approach.
Periodic and decaying solutions in discrete nonlinear Schrödinger with saturable nonlinearity
Authors: Pankov Alexander , Rothos Vassilis
Published: August 2008

We demonstrate the existence of solutions in the discrete nonlinear Schrödinger equation (DNLS) with saturable nonlinearity. We consider two types of solutions to DNLS periodic and vanishing at infinity. Calculus of variations and the Nehari manifolds are employed to establish the existence of these solutions. We present some extensions of our results, combining the Nehari manifold approach and the Mountain Pass argument.
Diversity increases biomass production for trematode parasites in snails
Authors: Hechinger Ryan F , Lafferty Kevin D , Kuris Armand M
Published: August 2008

Increasing species diversity typically increases biomass in experimental assemblages. But there is uncertainty concerning the mechanisms of diversity effects and whether experimental findings are relevant to ecological process in nature. Hosts for parasites provide natural, discrete replicates of parasite assemblages. We considered how diversity affects standing-stock biomass for a highly interactive parasite guild: trematode parasitic castrators in snails. In 185 naturally occurring habitat replicates (individual hosts), diverse parasite assemblages had greater biomass than single-species assemblages, including those of their most productive species. Additionally, positive diversity effects strengthened as species segregated along a secondary niche axis (space). The most subordinate species—also the most productive when alone—altered the general positive effect, and was associated with negative diversity effects on biomass. These findings, on a previously unstudied consumer class, extend previous research to illustrate that functional diversity and species identity may generally both explain how diversity influences biomass production in natural assemblages of competing species.
On the notion of ‘software independence’ in voting systems
Authors: Rivest Ronald L
Published: August 2008

This paper defines and explores the notion of ‘software independence’ in voting systems: ‘A voting system issoftware independentif an (undetected) change or error in its software cannot cause an undetectable change or error in an election outcome’. For example, optical scan and some cryptographically based voting systems are software independent. Variations and implications of this definition are explored. It is proposed that software-independent voting systems should be preferred, andsoftware-dependentvoting systems should be avoided.

An initial version of this paper was prepared for use by the Technical Guidelines Development Committee in their development of the Voluntary Voting System Guidelines, which will specify the requirements that the USA voting systems must meet to receive certification.
Peroxisomal Malate Dehydrogenase Is Not Essential for Photorespiration in Arabidopsis But Its Absence Causes an Increase in the Stoichiometry of Photorespiratory CO2 Release
Authors: Cousins Asaph B. , Pracharoenwattana Itsara , Zhou Wenxu , Smith Steven M. , Badger Murray R.
Published: August 2008

Peroxisomes are important for recycling carbon and nitrogen that would otherwise be lost during photorespiration. The reduction of hydroxypyruvate to glycerate catalyzed by hydroxypyruvate reductase (HPR) in the peroxisomes is thought to be facilitated by the production of NADH by peroxisomal malate dehydrogenase (PMDH). PMDH, which is encoded by two genes in Arabidopsis (Arabidopsis thaliana), reduces NAD+ to NADH via the oxidation of malate supplied from the cytoplasm to oxaloacetate. A double mutant lacking the expression of both PMDH genes was viable in air and had rates of photosynthesis only slightly lower than in the wild type. This is in contrast to other photorespiratory mutants, which have severely reduced rates of photosynthesis and require high CO2 to grow. The pmdh mutant had a higher O2-dependent CO2 compensation point than the wild type, implying that either Rubisco specificity had changed or that the rate of CO2 released per Rubisco oxygenation was increased in the pmdh plants. Rates of gross O2 evolution and uptake were similar in the pmdh and wild-type plants, indicating that chloroplast linear electron transport and photorespiratory O2 uptake were similar between genotypes. The CO2 postillumination burst and the rate of CO2 released during photorespiration were both greater in the pmdh mutant compared with the wild type, suggesting that the ratio of photorespiratory CO2 release to Rubisco oxygenation was altered in the pmdh mutant. Without PMDH in the peroxisome, the CO2 released per Rubisco oxygenation reaction can be increased by over 50%. In summary, PMDH is essential for maintaining optimal rates of photorespiration in air; however, in its absence, significant rates of photorespiration are still possible, indicating that there are additional mechanisms for supplying reductant to the peroxisomal HPR reaction or that the HPR reaction is altogether circumvented.
2-Benzyliminomethyl-6-bromo-4-chlorophenol
Authors: Pu Xiao-Hua
Published: August 2008

The title molecule, C14H11BrClNO, adopts a trans configuration with respect to the C=N double bond. The dihedral angle between the two aromatic rings is 70.4 (5)°. An intramolecular O—H...N hydrogen bond is observed between the hydroxyl and imine groups.
Ethyl 2-(3-benzoylthioureido)acetate
Authors: Hassan Ibrahim N. , Yamin Bohari M. , Kassim Mohammad B.
Published: August 2008

The title compound, C12H14N2O3S, adopts a cis–trans geometry of the thiourea group and is stabilized by intramolecular hydrogen bonds between the carbonyl O atoms and the H atom of the thioamide group and by a C—H...S interaction. Molecules are linked by two intermolecular hydrogen bonds (C—H...O and N—H...O), forming a one-dimensional chain parallel to the c axis.
Dimethyl 5-nitroisophthalate
Authors: Xie Min-Hao , Zou Pei , He Yong-Jun , Liu Ya-Ling , Huang Biao
Published: August 2008

The nitro group in the title compound, C10H9NO6, is rotated by 10.9 (5)° out of the plane of the benzene ring.
(2S,3S)-3-(4-Chlorophenyl)-8-methyltropane-2-carboxylic acid
Authors: Chen Zheng-Ping , Wang Song-Pei , Li Xiao-Min , Tang Jie , Lin Jian-Guo
Published: August 2008

In the title compound, C15H18ClNO2, the internal torsion angles of the tropane ring are comparable to those of tropane rings in the crystal structures reported for cocaine and its derivatives. There is an intramolecular hydrogen bond between the N atom in the tropane ring and the O atom of the carboxyl group. The crystal structure is further stabilized by many weak C—H...O interactions between the molecules in the ab plane, forming a two-dimensional supramolecular network.
1-[1-(4-Nitrophenyl)ethylidene]thiosemicarbazide
Authors: Wang Jian-Gang , Jian Fang-Fang , Ding Yu-Feng
Published: August 2008

The title compound, C9H10N4O2S, was prepared by the reaction of 1-(4-nitrophenyl)ethanone and thiosemicarbazide in ethanol at 367 K. There are weak intermolecular N—H...S and N—H...O hydrogen-bonding interactions in the crystal structure involving the amine and nitrile groups, respectively, as donors.
N,N′-Dicyclohexylnaphthalene-1,8;4:5-dicarboximide
Authors: Shukla Deepak , Rajeswaran Manju
Published: August 2008

The title compound, C26H26N2O4, synthesized by the reaction of naphthalene-1,4,5,8-tetracarboxylic acid anhydride and cyclohexylamine, exhibits good n-type semiconducting properties. Accordingly, thin-film transistor devices comprising this compound show n-type behavior with high field-effect electron moblity ca 6 cm2/Vs [Shukla, Nelson, Freeman, Rajeswaran, Ahearn, Meyer & Carey(2008). Chem. Mater. Submitted]. The asymmetric unit comprises one-quarter of the centrosymmetric molecule in which all but two methylene C atoms of the cyclohexane ring lie on a mirror plane; the point-group symmetry is 2/m. The naphthalenediimide unit is strictly planar, and the cyclohexane rings adopt chair conformations with the diimide unit in an equatorial position on each ring.
3α-Azido-5-cholestene
Authors: Houston Todd A. , Quader Sabina , Boyd Sue E. , Jenkins Ian D. , Healy Peter C.
Published: August 2008

The crystal structure of the title compound, C27H45N3, has been determined as part of our investigation into the hydrophobic modification of aminoglycoside antibiotics. The isopropyl group showed disorder for the tertiary carbon (equal occupancies), with high thermal motion for the peripheral atoms of the isopropyl and azide groups also apparent in the structure. The axial disposition of the azide group is consistent with the clean inversion of stereochemistry at C-3 under Mitsunobu conditions.
Size does matter: variation in herbivory between and within plants and the plant vigor hypothesis
Authors: Cornelissen Tatiana , Wilson Fernandes Geraldo , Vasconcellos‐Neto João
Published: August 2008

The plant stress and plant vigor hypotheses (PVH) are two of the most widely recognized hypothesis invoked to explain differential distribution of insect herbivores among their host plants. In both cases, the emphasis is on bottom–up processes (i.e. host‐plant quality), but a recent meta‐analytical review of the literature has shown that the plant stress hypothesis might have limited support among insect herbivores. In this study, we conducted a meta‐analysis of the effects of plant vigor on insect herbivore abundance and survivorship by reviewing 71 published articles that explicitly tested the PVH and enabled 161 independent comparisons. Z‐transform was used as the metric to standardize the results of all independent comparisons. Our quantitative results have shown that Hymenoptera (sawflies) was the most abundant group in the reviewed studies, representing 28.1% of the independent comparisons, followed by Diptera (25.1%) and Homoptera (22.6%). Amongst all the guilds studied, gall‐formers were the most representative group (68.0%), whereas leaf‐miners and stem‐borers were underrepresented (less than 4.0% of the available comparisons). Insect herbivores were significantly more abundant on more vigorous plants (E++=0.6432, CI=0.7558–0.7280), but no significant effect was detected on herbivore survivorship. When herbivores were categorized into feeding guilds, effects of plant vigor on herbivore abundance were stronger for sap‐suckers, leaf‐miners and gall‐formers. Our results have shown a strong herbivore preference for more vigorous plants, although our results do not support a preference–performance linkage.
Dynamics of grazing lawn formation: an experimental test of the role of scale‐dependent processes
Authors: Cromsigt Joris P. G. M. , Olff Han
Published: August 2008

Grazing lawns are characteristic for African savanna grasslands, standing out as intensely grazed patches of stoloniferous grazing‐tolerant grass species. Grazing lawn development has been associated with grazing and increased nutrient input by large migratory herds. However, we argue that in systems without mass migrations disturbances, other than direct grazing, drive lawn development. Such disturbances, e.g. termite activity or megaherbivore middens, also increase nutrient input and keep the bunch vegetation down for a prolonged time period. However, field observations show that not all such disturbances lead to grazing lawns. We hypothesize that the initial disturbance has to be of a minimal threshold spatial scale, for grazing intensity to be high enough to induce lawn formation. We experimentally tested this idea in natural tall savanna grassland. We mowed different‐sized plots to simulate initial disturbances of different scales (six times during one year) and applied fertilizer to half of the plots during two years to simulate increased nutrient input by herbivores or termite activity. Allowing grazing by naturally occurring herbivores, we followed the vegetation development over more than three years. Grazing kept bunch grass short in coarser, fertilized plots, while grasses grew out toward their initial height in fine‐scale and unfertilized plots. Moreover, lawn grasses strongly increased in cover in plots with an increased nutrient input but only after coarser scale disturbance. These results support our hypothesis that an increased nutrient input in combination with grazing indeed induces grazing lawn formation, but only above a threshold scale of the initial disturbance. Our results provide an alternative mechanism for the development of grazing lawns in systems that lack mass migrating herds. Moreover, it gives a new spatial dimension to the processes behind grazing lawn development, and hence help to understand how herbivores might create and maintain spatial heterogeneity in grassland systems.