bluuebunny/crossref_metadata_2025 huggingface dataset:
Silicon-based filters, resonators and acoustic channels with phononic crystal structures
Authors: Huang Zi-Gui
Published: June 2011

This paper discusses the phenomenon of phononic crystal silicon-based filters, resonators and acoustic channels structured in geometrical periodic arrays created by a single silicon material. Component structured geometrical periodic array refers to a structure of square stubbed rods arranged in repeated arrays on a silicon plate. The study discovered that the band gap of the phononic crystal structure can be modulated under different heights and rotational angles of periodically arrayed square stubbed rods. In addition to band gap modulation, we used the finite element method (FEM) and supercell techniques to analyse the resonance characteristics of defect-containing phononic crystal structures with a larger band gap size design. In addition, the paper also investigated the effects on acoustic channels. Previous studies have already analysed defect-containing resonator and channel phenomenon by the plane-wave expansion method with supercell techniques. However, the FEM can solve numerical issues of extreme difficulty to reach convergence. The results of this study elaborated on the manufacturing feasibility of silicon-based acoustic resonance and filter devices under a complementary metal–oxide–semiconductor synchronization process.
Scaling of spiking and humping in keyhole welding
Authors: Wei P S , Chuang K C , DebRoy T , Ku J S
Published: June 2011

Spiking, rippling and humping seriously reduce the strength of welds. The effects of beam focusing, volatile alloying element concentration and welding velocity on spiking, coarse rippling and humping in keyhole mode electron-beam welding are examined through scale analysis. Although these defects have been studied in the past, the mechanisms for their formation are not fully understood. This work relates the average amplitudes of spikes to fusion zone depth for the welding of Al 6061, SS 304 and carbon steel, and Al 5083. The scale analysis introduces welding and melting efficiencies and an appropriate power distribution to account for the focusing effects, and the energy which is reflected and escapes through the keyhole opening to the surroundings. The frequency of humping and spiking can also be predicted from the scale analysis. The analysis also reveals the interrelation between coarse rippling and humping. The data and the mechanistic findings reported in this study are useful for understanding and preventing spiking and humping during keyhole mode electron and laser beam welding.
Numerical and experimental investigation of fishnet-based metamaterial in a X-band waveguide
Authors: Sabah C , Roskos H G
Published: June 2011

In this paper, a fishnet-based metamaterial for the microwave X-band frequencies is introduced and investigated both numerically and experimentally. The main innovation introduced here is that the structure is composed of dielectric and metallic parts in such a way that there is no connection between the metallic part of the metamaterial and the waveguide. The homogeneous-effective-medium theory is employed for the characterization of the structure. A left-handed region is identified using the simulated and experimental results. The performance of the structure is described by a figure-of-merit calculation. The measured results are in good agreement with the simulated ones which show that the proposed metamaterial operates well like a fishnet metamaterial at around 10 GHz.
Cathodoluminescence microcharacterization of the radiation-sensitive defect microstructure of in situ buried oxide in silicon
Authors: Stevens-Kalceff Marion A
Published: June 2011

Cathodoluminescence (CL) spectroscopy in a scanning electron microscope has been used to investigate the radiation-sensitive defect structure of the buried amorphous oxide layer produced by oxygen ion implantation in silicon (Si⟨1 0 0⟩) in comparison with bulk amorphous silicon dioxide (a-SiO2). CL microanalysis allows the defect structure of the buried oxide (BOX) layer to be investigated without removal of the silicon-on-insulator (SOI) top layer. CL emissions are observed at 1.63, 2.10, 2.31 and 2.66 eV and are associated with silicon clusters and nanoparticles that form in the BOX as a result of the post-implantation, high-temperature anneal. CL emission at ∼3 eV may be associated with excess silicon and/or inclusions of high-pressure crystalline SiO2 polymorph (coesite) in the BOX near the SiO2–Si substrate. A partially resolved CL emission may also be observed at 1.88 eV and is possibly associated with a native non-bridging oxygen defect of SiO2. CL emission from the confined strained BOX is dominated by defects associated with large surface-to-volume ratio nanoscale silicon clusters and their interfaces. CL spectra from the in situ BOX are electron radiation sensitive. Electron irradiation results in localized trapped charge-induced electric fields which are enhanced within the strained confined BOX layer at nanoscale silicon cluster defects and interfaces. These enhanced electric fields and residual strain near the interfaces can contribute to breakdown of the BOX.
Performance of different tungsten grades under transient thermal loads
Authors: Linke J. , Loewenhoff T. , Massaut V. , Pintsuk G. , Ritz G. , Rödig M. , Schmidt A. , Thomser C. , Uytdenhouwen I. , Vasechko V. , Wirtz M.
Published: June 2011

Plasma facing components in future thermonuclear fusion devices will be subjected to intense transient thermal loads due to type I edge localized modes (ELMs), plasma disruptions, etc. To exclude irreversible damage to the divertor targets, local energy deposition must remain below the damage threshold for the selected wall materials. For monolithic tungsten (pure tungsten and tungsten alloys) power densities above ≈0.3 GW m−2 with 1 ms duration result in the formation of a dense crack network. Thin tungsten coatings for the so-called ITER-like wall in JET, which have been deposited on a two-directional carbon–fibre composite (CFC) material, are even less resistant to thermal shock damage; here the threshold values are by a factor of 2 lower. First ELM-simulation experiments with high cycle numbers up to 104 cycles on actively cooled bulk tungsten targets do not reveal any cracks for absorbed power densities up to 0.2 GW m−2 and ELM-durations in the sub-millisecond range (0.8 ms); at somewhat higher power densities (0.27 GW m−2, Δt = 0.5 ms) cracks have been detected for 106 cycles.
Impact of off-axis RF current drive on JET advanced scenarios
Authors: Garcia J. , Giruzzi G. , Litaudon X. , Mailloux J. , Artaud J.F. , Basiuk V. , Decker J. , Imbeaux F. , Peysson Y. , Schneider M.
Published: June 2011

The impact of the radio-frequency heating and current drive systems on JET advanced scenarios at high density is analysed by means of the CRONOS suite of codes for integrated tokamak modelling. In particular, the performance of the proposed electron cyclotron heating and current drive system for JET is evaluated. As a first step, the code is applied in the interpretative mode to analyse two high power advanced scenario discharges of JET, in order to validate both the heating and current drive computational modules and the overall simulation procedure. Then, JET advanced scenarios are studied by predictive simulations on the basis of previous results. The simulations show that lower hybrid and electron cyclotron heating and current drive systems can together provide off-axis current in order to create and sustain steady-state scenarios on JET at high density. These results give deeper insight into the future advanced scenarios in ITER, since they establish a clear way to test some key aspects of them in present day devices such as JET.
Overlapping kinetochore targets of CK2 and Aurora B kinases in mitotic regulation
Authors: Peng Yutian , Wong Catherine C. L. , Nakajima Yuko , Tyers Randall G. , Sarkeshik Ali S. , Yates John , Drubin David G. , Barnes Georjana
Published: June 2011

Protein kinase CK2 is one of the most conserved kinases in eukaryotic cells and plays essential roles in diverse processes. While we know that CK2 plays a role(s) in cell division, our understanding of how CK2 regulates cell cycle progression is limited. In this study, we revealed a regulatory role for CK2 in kinetochore function. The kinetochore is a multi-protein complex that assembles on the centromere of a chromosome and functions to attach chromosomes to spindle microtubules. To faithfully segregate chromosomes and maintain genomic integrity, the kinetochore is tightly regulated by multiple mechanisms, including phosphorylation by Aurora B kinase. We found that a loss of CK2 kinase activity inhibits anaphase spindle elongation and results in chromosome missegregation. Moreover, a lack of CK2 activates the spindle assembly checkpoint. We demonstrate that CK2 associates with Mif2, the Saccharomyces cerevisiae homologue of human CENP-C, which serves as an important link between the inner and outer kinetochore. Furthermore, we show Mif2 and the inner kinetochore protein Ndc10 are phosphorylated by CK2, and this phosphorylation plays antagonistic and synergistic roles with Aurora B phosphorylation of these targets, respectively.
LinkinPath: from sequence to interconnected pathway
Authors: Ingsriswang Supawadee , Yokwai Sunai , Wichadakul Duangdao
Published: June 2011

Summary: LinkinPath is a pathway mapping and analysis tool that enables users to explore and visualize the list of gene/protein sequences through various Flash-driven interactive web interfaces including KEGG pathway maps, functional composition maps (TreeMaps), molecular interaction/reaction networks and pathway-to-pathway networks. Users can submit single or multiple datasets of gene/protein sequences to LinkinPath to (i) determine the co-occurrence and co-absence of genes/proteins on animated KEGG pathway maps; (ii) compare functional compositions within and among the datasets using TreeMaps; (iii) analyze the statistically enriched pathways across the datasets; (iv) build the pathway-to-pathway networks for each dataset; (v) explore potential interaction/reaction paths between pathways; and (vi) identify common pathway-to-pathway networks across the datasets.

Availability: LinkinPath is freely available to all interested users at http://www.biotec.or.th/isl/linkinpath/.

Contact:  supawadee@biotec.or.th

Supplementary information:  Supplementary data are available at Bioinformatics online.
Role of Hydroxycinnamic Acids in the Infection of Maize Silks by Fusarium graminearum Schwabe
Authors: Cao Ana , Reid Lana M. , Butrón Ana , Malvar Rosa Ana , Souto Xose C. , Santiago Rogelio
Published: June 2011

In the current study, the hydroxycinnamic acids in silks of diverse maize inbred lines differing in Fusarium resistance were determined at several times after inoculation with Fusarium graminearum or sterile water as control. The main objective was to determine the possible relationship between the hydroxycinnamic acid changes in silks and ear rot resistance. Several changes in the cell-wall-bound hydroxycinnamic acid concentrations were observed after inoculation with F. graminearum, although these changes were not directly correlated with genotypic resistance to this fungus. Ester-bound ferulic acid decreased, probably due to degradation of hemicellulose by hydrolytic enzymes produced by Fusarium spp., while p-coumaric acid and diferulates showed slight increases that, in conjunction, did not result in delayed F. graminearum progression through the silks. It is important to note that the decrease of ferulic acid in the F. graminearum treatment was faster in susceptible than in resistant genotypes, suggesting a differential hemicellulose degradation in silk tissues. Therefore, the ability of the maize genotypes to slow down that process through hemicellulose structural features or xylanase inhibitors needs to be addressed in future studies.
First Report of Pepino mosaic virus Infecting Tomato in Mexico
Authors: Ling K.-S. , Zhang W.
Published: June 2011

Pepino mosaic virus (PepMV) (genus Potexvirus) was first reported in Europe to be infecting greenhouse tomatoes (Solanum lycopersicum) in 2000 (3). Subsequently, it has also been identified in Canada and the United States (1) and has become widespread on greenhouse tomatoes in many countries. In early spring of 2010, symptoms including chlorotic mosaic or chlorotic patches on leaves, necrotic stems, and fruit deformation or marbling were noted. Approximately 50% of plants in a greenhouse in Jocotitlan, Mexico exhibited symptoms. Twenty-three symptomatic samples in four separate collections between April 2010 and January 2011 all tested positive for the presence of PepMV by ELISA and/or Agristrips (BioReba, Switzerland). Two symptomless samples were negative for PepMV. Biological inoculation with the isolate MX10-05 to three Nicotiana benthamiana and three tomato cv. Horizon plants all resulted in chlorotic mosaic symptoms on the systemic leaves and PepMV on the inoculated plants was confirmed by ELISA. To determine the genotype of PepMV in MX10-05, two primer sets targeting different part of the virus genome (separated by 2,744 nt) were selected for reverse transcription (RT)-PCR using total plant RNA extracted with the RNeasy Plant Mini Kit (Qiagen, Valencia, CA). A RT-PCR product (840 bp) was obtained using the first primer set (PepMV-Ch2.F541: 5′CATGGAACCAGCTGATGTGA and PepMV-Ch2.R1380: 5′TCTTTGTATATGGTCGCAGC) targeting the 5′ portion of the RNA-dependent RNA polymerase (RdRp) gene. The PCR product was cloned in pCR2.1 using the TOPO TA cloning system (Invitrogen, Carlsbad, CA) and a single clone was sequenced in both directions (Functional Biosciences, Madison, WI). After primer trimming, the 800-bp sequence (GenBank Accession No. JF811600) was shown in BLASTn to have its highest nucleotide sequence identity (99.4%) to the type PepMV-CH2 (DQ000985), 98% to other CH2/US2 isolates, 85% to US1, and 84% to EU. Another RT-PCR product (also 840 bp) was generated using the second primer set (PepMV-Ch2.F4081: 5′AAAAACGCTGTACCCAAAAC and PepMV-Ch2.R4920: 5′CAGAAATGTGTTCAGAGGGG) targeting the 3′ portion of RdRp and TGB1 genes. This second genome segment enables the differentiation of the CH2 and US2 genotypes. The resulting 800 bp (JF811600) had the highest nucleotide sequence identity (99.5%) to the type PepMV CH2, 97% to other CH2 isolates, 83% to US2, and only 81% to the EU genotype. Taken together, these sequence analyses support the identification of MX10-05 as a PepMV-CH2 isolate (2). However, the presence of other PepMV genotypes cannot be excluded once sequences from other isolates are obtained and analyzed. To our knowledge, this is the first report of PepMV on greenhouse tomatoes in Mexico.

References: (1). C. J. French et al. Plant Dis. 85:1121, 2001. (2). K.-S. Ling. Virus Genes 34:1, 2007. (3). R. A. A. van der Vlugt et al. Plant Dis. 84:103, 2000.
A Model to Estimate the Amount of Primary Inoculum of Elsinoë ampelina
Authors: Carisse Odile , Lefebvre Annie
Published: June 2011

In Eastern Canada, anthracnose, caused by the fungus Elsinoë ampelina, is a serious disease on susceptible grape cultivars. In the absence of management tools, anthracnose management relies almost exclusively on fungicide applications programmed at fixed intervals. Therefore, a better understanding of the factors affecting primary inoculum release and abundance would help in the timing of the first fungicide applications. The temporal dynamics of airborne primary inoculum released from cane cankers were investigated from 2007 to 2010. One to three times per week, starting in the first week of April, six 12-cmlong cane pieces were randomly selected from diseased canes that had overwintered on a vineyard floor. The concentration of E. ampelina conidia was expressed as the number of conidia per square millimeter of canker. In total, 27, 32, 33, and 118 samplings were conducted in 2007, 2008, 2009, and 2010, respectively, with the 118 samplings conducted on three sites at 49, 35, and 34 samplings for site 1, 2, and 3, respectively. Each year, the number of conidia per square millimeter of canker was expressed as the proportion of seasonal inoculum (PSI) at the same site and analyzed as a function of degree-days (DD; base temperature = 0°C) accumulated since 1 April (cumulative degreedays [CDD]). The nonlinear sigmoid model in the form PSI = 1.003/(1 + e–((CDD – 566.133)/139.204)) provided adequate fit to the observed data (P < 0.0001, R2 = 0.97). When the model was validated against independent data, the model adequately predicted PSI; however, reliability was improved by adding a “dry days” threshold of 6 days during which accumulation of DD is stopped. This study shows that primary inoculum of grape anthracnose is available early in the season before bud break; meaning that emerging leaves could be infected provided that weather conditions are favorable. The results also show that there is an overlap in the availability of primary and secondary inoculum, mainly during the period of rapid leaf growth, a situation that may explain the explosive nature of the disease. The results suggest that, on susceptible cultivars and when there is a history of anthracnose in the vineyard, a fungicide spray program should be initiated early in the season, as soon as leaves are present.
Biofilm formation by zygomycetes: quantification, structure and matrix composition
Authors: Singh Rachna , Shivaprakash M. R. , Chakrabarti Arunaloke
Published: June 2011

Most studies on fungal biofilms have focused onCandidain yeasts andAspergillusin mycelial fungi. To the authors’ knowledge, biofilm formation by zygomycetes has not been reported previously. In this study, the biofilm-forming capacity ofRhizopus oryzae,Lichtheimia corymbifera,Rhizomucor pusillusandApophysomyces eleganswas evaluated.At appropriate seeding spore densities,Rhp. oryzae(105c.f.u. ml−1),L. corymbifera(104c.f.u. ml−1) andRhm. pusillus(104c.f.u. ml−1) produced highly intertwined, adherent structures on flat-bottomed polystyrene microtitre plates after 24 h at 37 °C. The adhered fungal hyphae were encased in an extracellular matrix, as confirmed by phase-contrast and confocal microscopy. The thickness ofRhp. oryzae,L. corymbiferaandRhm. pusillusbiofilms was 109.67±10.02, 242±23.07 and 197±9.0 µm (mean±sd), respectively. Biochemical characterization of the biofilm matrix indicated the presence of glucosamine, constituting 74.54–82.22 % of its dry weight,N-acetylglucosamine, glucose and proteins. Adherence and biofilm formation were not observed inA. elegans. AlthoughA. elegansspores germinated at all three seeding densities tested (1×107, 1×106and 1×105c.f.u. ml−1), no significant difference was observed (P>0.05) between theA490of wells inoculated withA. elegansand the cut-offA490for biofilm detection. This study highlights the potential for biofilm formation by at least three medically important species of zygomycetes.
Alleles A and B of non-structural protein 1 of avian influenza A viruses differentially inhibit beta interferon production in human and mink lung cells
Authors: Munir Muhammad , Zohari Siamak , Metreveli Giorgi , Baule Claudia , Belák Sándor , Berg Mikael
Published: June 2011

Non-structural protein 1 (NS1) counteracts the production of host type I interferons (IFN-α/β) for the efficient replication and pathogenicity of influenza A viruses. Here, we reveal another dimension of the NS1 protein of avian influenza A viruses in suppressing IFN-β production in cultured cell lines. We found that allele A NS1 proteins of H6N8 and H4N6 have a strong capacity to inhibit the activation of IFN-β production, compared with allele B from corresponding subtypes, as measured by IFN stimulatory response element (ISRE) promoter activation, IFN-β mRNA transcription and IFN-β protein expression. Furthermore, the ability to suppress IFN-β promoter activation was mapped to the C-terminal effector domain (ED), while the RNA-binding domain (RBD) alone was unable to suppress IFN-β promoter activation. Chimeric studies indicated that when the RBD of allele A was fused to the ED of allele B, it was a strong inhibitor of IFN-β promoter activity. This shows that well-matched ED and RBD are crucial for the function of the NS1 protein and that the RBD could be one possible cause for this differential IFN-β inhibition. Notably, mutagenesis studies indicated that the F103Y and Y103F substitutions in alleles A and B, respectively, do not influence the ISRE promoter activation. Apart from dsRNA signalling, differences were observed in the expression pattern of NS1 in transfected human and mink lung cells. This study therefore expands the versatile nature of the NS1 protein in inhibiting IFN responses at multiple levels, by demonstrating for the first time that it occurs in a manner dependent on allele type.
Antigen-presenting cells of haematopoietic origin prime cytomegalovirus-specific CD8 T-cells but are not sufficient for driving memory inflation during viral latency
Authors: Seckert Christof K. , Schader Sina I. , Ebert Stefan , Thomas Doris , Freitag Kirsten , Renzaho Angélique , Podlech Jürgen , Reddehase Matthias J. , Holtappels Rafaela
Published: June 2011

Expansion of the CD8 T-cell memory pool, also known as ‘memory inflation’, for certain but not all viral epitopes in latently infected host tissues is a special feature of the immune response to cytomegalovirus. The Ld-presented murine cytomegalovirus (mCMV) immediate–early (IE) 1 peptide is the prototype of an epitope that is associated with memory inflation. Based on the detection of IE1 transcripts in latently infected lungs it was previously proposed that episodes of viral gene expression and antigenic activity due to desilencing of a limited number of viral genes may drive epitope-specific memory inflation. This would imply direct antigen presentation through latently infected host tissue cells rather than cell death-associated cross-presentation of viral antigens derived from productively infected cells through uninfected, professional antigen-presenting cells (profAPCs). To address the role of bone marrow-derived profAPCs in CD8 T-cell priming and memory to mCMV, we have used here a combined sex-mismatched and MHC class-I mismatched dual-marker bone marrow chimera model in which presentation of the IE1 epitope is restricted to donor-derived sry
+Ld+ cells of haematopoietic differentiation lineages. Successful CD8 T-cell priming specific for the Ld- and Dd-presented inflationary epitopes IE1 and m164, respectively, but selective failure in IE1 epitope-specific memory inflation in these chimeras indicates different modes of antigen presentation involved in CD8 T-cell priming and memory inflation. These data suggest that memory inflation during mCMV latency requires expression of the epitope-presenting MHC class-I molecule by latently infected non-haematopoietic host tissue cells and thus predicts a role for direct antigen presentation in memory inflation.
Genetic diversification of H5N1 highly pathogenic avian influenza A virus during replication in wild ducks
Authors: Watanabe Yohei , Ibrahim Madiha S. , Ellakany Hany F. , Abd El-Hamid Hatem S. , Ikuta Kazuyoshi
Published: June 2011

Highly pathogenic avian influenza A virus subtype H5N1 can potentially generate novel variants during replication of infected hosts. To determine which H5N1 variants predominate in wild birds, we determined the sequences of RT-PCR amplified viral genes from several organs of infected chickens and ducks from Egypt, where H5N1 outbreaks in birds are endemic. Comparison of the sequences in viruses from trachea, lung, brain and liver revealed diversification with different amino acid substitutions in different ducks, but no diversification in chickens. These specific amino acid substitutions were rare among viruses currently circulating in Egypt. In addition, the H5N1 variants showed distinct growth kinetics in duck, canine and human cells. Our findings suggested that ducks can generate H5N1 variants with novel amino acid substitutions that might serve as aetiological agents for new influenza virus outbreaks and epidemics.
Mutations in the G–H loop region of ephrin-B2 can enhance Nipah virus binding and infection
Authors: Yuan Junfa , Marsh Glenn , Khetawat Dimple , Broder Christopher C. , Wang Lin-Fa , Shi Zhengli
Published: June 2011

Nipah virus (NiV) and Hendra virus (HeV) are zoonotic paramyxoviruses classified in the genus Henipavirus of the family Paramyxoviridae. The entry of henipaviruses occurs through a pH-independent membrane-fusion mechanism mediated by the cooperation of the viral attachment (G) and fusion (F) envelope glycoproteins following virion binding to susceptible host cells. Virus attachment is mediated by the interaction of the G glycoprotein with ephrin-B2 or ephrin-B3, which were identified as the functional receptors of henipavirus. Several residues of the G glycoprotein that are important for receptor binding have been determined through mutagenesis and structural analyses; however, similar approaches have not been carried out for the viral receptor ephrin-B2. Here, an alanine-scanning mutagenesis analysis was performed to identify residues of ephrin-B2 which are critical for NiV binding and entry by using an NiV-F- and -G-glycoprotein pseudotyped lentivirus assay. Results indicated that the G–H loop of ephrin-B2 was indeed critical for the interaction between ephrin-B2 and NiV-G. Unexpectedly, however, some alanine-substitution mutants located in the G–H loop enhanced the infectivity of the NiV pseudotypes, in particular an L124A mutation enhanced entry >30-fold. Further analysis of the L124A ephrin-B2 mutant demonstrated that an increased binding affinity of the mutant receptor with NiV-G was responsible for the enhanced infectivity of both pseudovirus and infectious virus. In addition, cell lines that were stably expressing the L124A mutant receptor were able to support NiV infection more efficiently than the wild-type molecule, potentially providing a new target-cell platform for viral isolation or virus-entry inhibitor screening and discovery.
Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells
Authors: Yu Hong-Bing , Johnson Rory , Kunarso Galih , Stanton Lawrence W.
Published: June 2011

The differentiation of pluripotent embryonic stem cells is regulated by networks of activating and repressing transcription factors that orchestrate determinate patterns of gene expression. With the recent mapping of target sites for many transcription factors, it has been a conundrum that so few of the genes directly targeted by these factors are transcriptionally responsive to the binding of that factor. To address this, we generated genome-wide maps of the transcriptional repressor REST and five of its corepressors in mouse embryonic stem cells. Combining these binding-site maps with comprehensive gene-expression profiling, we show that REST is functionally heterogeneous. Approximately half of its binding sites apparently are nonfunctional, having weaker binding of REST and low recruitment of corepressors. In contrast, the other sites strongly recruit REST and corepressor complexes with varying numbers of components. Strikingly, the latter sites account for almost all observed gene regulation. These data support a model where productive gene repression by REST requires assembly of a multimeric “repressosome” complex, whereas weak recruitment of REST and its cofactors is insufficient to repress gene expression.
Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis
Authors: Bogdanović Ozren , Long Steven W. , van Heeringen Simon J. , Brinkman Arie B. , Gómez-Skarmeta Jose Luis , Stunnenberg Hendrik G. , Jones Peter L. , Veenstra Gert Jan C.
Published: June 2011

DNA methylation is a tightly regulated epigenetic mark associated with transcriptional repression. Next-generation sequencing of purified methylated DNA obtained from early Xenopus tropicalis embryos demonstrates that this genome is heavily methylated during blastula and gastrula stages. Although DNA methylation is largely absent from transcriptional start sites marked with histone H3 lysine 4 trimethylation (H3K4me3), we find both promoters and gene bodies of active genes robustly methylated. In contrast, DNA methylation is absent in large H3K27me3 domains, indicating that these two repression pathways have different roles. Comparison with chromatin state maps of human ES cells reveals strong conservation of epigenetic makeup and gene regulation between the two systems. Strikingly, genes that are highly expressed in pluripotent cells and in Xenopus embryos but not in differentiated cells exhibit relatively high DNA methylation. Therefore, we tested the repressive potential of DNA methylation using transient and transgenic approaches and show that methylated promoters are robustly transcribed in blastula- and gastrula-stage embryos, but not in oocytes or late embryos. These findings have implications for reprogramming and the epigenetic regulation of pluripotency and differentiation and suggest a relatively open, pliable chromatin state in early embryos followed by reestablished methylation-dependent transcriptional repression during organogenesis and differentiation.
Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions
Authors: Zentner Gabriel E. , Tesar Paul J. , Scacheri Peter C.
Published: June 2011

Epigenetic regulation of gene enhancer elements is important for establishing and maintaining the identity of cells. Gene enhancer elements are thought to exist in either active or poised states distinguishable by chromatin features, but a complete understanding of the regulation of enhancers is lacking. Here, by using mouse embryonic stem cells and their differentiated derivatives, as well as terminally differentiated cells, we report the coexistence of multiple, defined classes of enhancers that serve distinct cellular functions. Specifically, we found that active enhancers can be subclassified based on varying levels of H3K4me1, H3K27ac, and H3K36me3 and the pSer2/5 forms of RNA polymerase II. The abundance of these histone modifications positively correlates with the expression of associated genes and cellular functions consistent with the identity of the cell type. Poised enhancers can also be subclassified based on presence or absence of H3K27me3 and H3K9me3, conservation, genomic location, expression levels of associated genes, and predicted function of associated genes. These findings not only refine the repertoire of histone modifications at both active and poised gene enhancer elements but also raise the possibility that enhancers associated with distinct cellular functions are partitioned based on specific combinations of histone modifications.
Extracellular Nucleotides and Apyrases Regulate Stomatal Aperture in Arabidopsis
Authors: Clark Greg , Fraley Devin , Steinebrunner Iris , Cervantes Andrew , Onyirimba James , Liu Angela , Torres Jonathan , Tang Wenqiang , Kim Joshua , Roux Stanley J.
Published: June 2011

This study investigates the role of extracellular nucleotides and apyrase enzymes in regulating stomatal aperture. Prior data indicate that the expression of two apyrases in Arabidopsis (Arabidopsis thaliana), APY1 and APY2, is strongly correlated with cell growth and secretory activity. Both are expressed strongly in guard cell protoplasts, as determined by reverse transcription-polymerase chain reaction and immunoblot analyses. Promoter activity assays for APY1 and APY2 show that expression of both apyrases correlates with conditions that favor stomatal opening. Correspondingly, immunoblot data indicate that APY expression in guard cell protoplasts rises quickly when these cells are moved from darkness into light. Both short-term inhibition of ectoapyrase activity by polyclonal antibodies and long-term suppression of APY1 and APY2 transcript levels significantly disrupt normal stomatal behavior in light. Stomatal aperture shows a biphasic response to applied adenosine 5′-[γ-thio]triphosphate (ATPγS) or adenosine 5′-[β-thio] diphosphate, with lower concentrations inducing stomatal opening and higher concentrations inducing closure. Equivalent concentrations of adenosine 5′-O-thiomonophosphate have no effect on aperture. Two mammalian purinoceptor inhibitors block ATPγS- and adenosine 5′-[β-thio] diphosphate-induced opening and closing and also partially block the ability of abscisic acid to induce stomatal closure and of light to induce stomatal opening. Treatment of epidermal peels with ATPγS induces increased levels of nitric oxide and reactive oxygen species, and genetically suppressing the synthesis of these agents blocks the effects of nucleotides on stomatal aperture. A luciferase assay indicates that treatments that induce either the closing or opening of stomates also induce the release of ATP from guard cells. These data favor the novel conclusion that ectoapyrases and extracellular nucleotides play key roles in regulating stomatal functions.
Abnormal liver tests in people aged 75 and above: prevalence and association with mortality
Authors: Fleming K. M. , West J. , Aithal G. P. , Fletcher A. E.
Published: June 2011

Aliment Pharmacol Ther 2011; 34: 324–334

Background  Despite their common use the occurrence and consequences of abnormal liver tests remain unclear.

Aims  To estimate the prevalence and mortality associated with abnormal liver tests in people aged 75 years and above.

Methods  A cohort study on 13 276 people aged 75 years and above, registered with general practices, with a valid measurement of one or more liver test, calculating the prevalence of abnormal aspartate transaminase (AST), alkaline phosphatase (ALP) or bilirubin. Hazard ratios (HRs) were calculated for all‐cause and cause‐specific mortality comparing elderly patients with abnormal liver tests to elderly patients with normal liver tests.

Results  At least one abnormal liver test was found in 2175 subjects (16.1%, 95% CI [15.4%, 16.7%]). The prevalence of a single abnormal liver test was 3.3% (95% CI [3.0%, 3.7%]) for AST, 9.2% (95% CI [8.8%, 9.7%]) for ALP and 5.4% (95% CI [5.1%, 5.9%]) for bilirubin. Abnormal AST, ALP and bilirubin were associated with increased risks of all‐cause mortality; adjusted HRs, 1.27(95% CI [1.09, 1.47]), 1.47(95% CI [1.35, 1.61]) and 1.15(95% CI [1.02, 1.30]), respectively. Abnormal AST and ALP were associated with sevenfold and sixfold increased risk of death from liver disease, respectively. Two or more abnormal liver tests were associated with 2‐fold and 17‐fold increased risk of death from cancer and liver disease, respectively. Of the causes examined, absolute mortality rates were highest for cardiovascular disease in subjects with and without abnormal liver tests.

Conclusions  Abnormal liver tests occur commonly in elderly people and are associated with a modest increase in all‐cause mortality. There was a strong association with liver disease; however, the majority of deaths were not due to this cause.
Growth Rate Hypothesis does not apply across colimiting conditions: cholesterol limitation affects phosphorus homoeostasis of an aquatic herbivore
Authors: Lukas Marcus , Sperfeld Erik , Wacker Alexander
Published: June 2011

1. Herbivores show stronger control of element homoeostasis than primary producers, which can lead to constraints in carbon and nutrient transfer efficiencies from plants to animals. Insufficient dietary phosphorus (P) availability can cause reduced body P contents along with lower growth rates of animals, leading to a positive relationship between growth and body P.

2. We examined how a second limiting food component in combination with dietary P limitation influences growth and P homoeostasis of a herbivore and how this colimitation influences the hypothesized positive correlation between body P content and growth rates. Therefore, we investigated the responses in somatic growth and P stoichiometry of Daphnia magna raised on a range of diets with different amounts of P and the sterol cholesterol.

3. Somatic growth rates of D. magna increased asymptotically with increasing P as well as with increasing cholesterol availability. The body P content increased with increasing dietary P and stabilized at high dietary P availability. The observed plasticity in D. magna’s P stoichiometry became stronger with increasing cholesterol availability, i.e. with decreasing colimitation by cholesterol.

4. At P‐limiting conditions, the positive correlation between body P content and growth rate, as predicted by the growth rate hypothesis (GRH) applied to the within‐species level, declined with increasing cholesterol limitation and disappeared entirely when cholesterol was not supplied. Thus, even when Daphnia shows no growth response owing to strong limitation by the colimiting nutrient, the body P content may vary substantially, calling into question the unconditional use of herbivores’ P content as predictor of a potential P limitation in nature.

5. The observed interaction between dietary P and cholesterol on Daphnia’s growth and stoichiometry can be used as a conceptual framework of how colimiting essential nutrients affect herbivore homoeostasis, and provide further insights into the applicability of the GRH within a consumer species.
The translational regulatory function of SecM requires the precise timing of membrane targeting
Authors: Yap Mee‐Ngan , Bernstein Harris D.
Published: June 2011

In Escherichia coli, secA expression is regulated at the translational level by an upstream gene (secM) that encodes a presecretory protein. SecM contains a C‐terminal sequence motif that induces a transient translation arrest. Inhibition of SecM membrane targeting prolongs the translation arrest and increases SecA synthesis by concomitantly altering the structure of the secM–secA mRNA. Here we show that the SecM signal peptide plays an essential role in this regulatory process by acting as a molecular timer that co‐ordinates membrane targeting with the synthesis of the arrest motif. We found that signal peptide mutations that alter targeting kinetics and insertions or deletions that change the distance between the SecM signal peptide and the arrest motif perturb the balance between the onset and release of arrest that is required to regulate SecA synthesis. Furthermore, we found that the strength of the interaction between the ribosome and the SecM arrest motif is calibrated to ensure the release of arrest upon membrane targeting. Our results strongly suggest that several distinctive features of the SecM protein evolved as a consequence of constraints imposed by the ribosome and the Sec machinery.
Induction of telomere‐mediated chromosomal truncation and stability of truncated chromosomes in Arabidopsis thaliana
Authors: Teo Chee How , Ma Lu , Kapusi Eszter , Hensel Götz , Kumlehn Jochen , Schubert Ingo , Houben Andreas , Mette Michael Florian
Published: June 2011

Minichromosomes possess functional centromeres and telomeres and thus should be stably inherited. They offer an enormous opportunity to plant biotechnology as they have the potential to simultaneously transfer and stably express multiple genes. Segregating independently of host chromosomes, they provide a platform for accelerating plant breeding. Following a top‐down approach, we truncated endogenous chromosomes in Arabidopsis thaliana by Agrobacterium‐mediated transfer of T‐DNA constructs containing telomere sequences. Blocks of A. thaliana telomeric repeats were inserted into a binary vector suitable for stable transformation. After transfer of these constructs into the natural tetraploid A. thaliana accession Wa‐1, chromosome truncation by T‐DNA‐induced de novo formation of telomeres could be confirmed by DNA gel blot analysis, PCR (polymerase chain reaction), and fluorescence in situ hybridisation. The addition of new telomere repeats in this process could start alternatively from within the T‐DNA‐derived telomere repeats or from adjacent sequences close to the right border of the T‐DNA. Truncated chromosomes were transmissible in sexual reproduction, but were inherited at rates lower than expected according to Mendelian rules.
Knockdown of CENH3 in Arabidopsis reduces mitotic divisions and causes sterility by disturbed meiotic chromosome segregation
Authors: Lermontova Inna , Koroleva Olga , Rutten Twan , Fuchs Joerg , Schubert Veit , Moraes Izabel , Koszegi David , Schubert Ingo
Published: June 2011

The histone H3 variant (CENH3) of centromeric nucleosomes is essential for kinetochore assembly and thus for chromosome segregation in eukaryotes. The mechanism(s) that determine centromere identity, assembly and maintenance of kinetochores are still poorly understood. Although the role of CENH3 during mitosis has been studied in several organisms, little is known about its meiotic function. We show that RNAi‐mediated CENH3 knockdown in Arabidopsis thaliana caused dwarfism as the result of a reduced number of mitotic divisions. The remaining mitotic divisions appeared to be error‐free. CENH3 RNAi transformants had reduced fertility because of frequently disturbed meiotic chromosome segregation. N‐terminally truncated EYFP–CENH3(C) is deposited to and functional within Arabidopsis centromeres of mitotic chromosomes, but cannot be loaded onto centromeres of meiotic nuclei. Thus the N‐terminal part is apparently required for CENH3 loading during meiosis. EYFP–CENH3(C) expression reduces the amount of endogenous CENH3, thus mimicking the effect of RNAi. The consequences of reduced endogenous CENH3 and lack of meiotic incorporation of EYFP–CENH3(C) are reduced fertility caused by insufficient CENH3 loading to the centromeres of meiotic chromosomes, subsequent lagging of chromosomes and formation of micronuclei.
Carbohydrate dynamics in roots and rhizomes of Cirsium arvense and Tussilago farfara
Authors: NKURUNZIZA L , STREIBIG J C
Published: June 2011

Nkurunziza L & Streibig JC (2011). Carbohydrate dynamics in roots and rhizomes of Cirsium arvense and Tussilago farfara. Weed Research51, 461–468.

Information on the source–sink dynamics of carbohydrates during early plant growth can indicate when perennial weeds are most vulnerable to mechanical control. In this study, carbohydrate contents in the roots or rhizomes of two noxious perennial weeds, Cirsium arvense and Tussilago farfara, and basipetal translocation of photo‐assimilates were measured. We used HPLC for carbohydrate measurements and 14C labelling to follow the translocation of photo‐assimilates during early growth. These measurements were related to leaf number and leaf area. Fructan and fructose changed significantly over the experimental periods. Fructan for both species was greatest within 2 weeks after planting 5‐cm‐long root/rhizome fragments and declined thereafter. After 2 weeks, fructose concentrations, which were at their minimum level at planting time, rose sharply because of fructan depolymerisation. The radioactive carbon applied to the aerial parts translocated rapidly to root or rhizome systems around 500–600 d °C after emergence. We concluded that while the fructan was continuously depleted in the roots or rhizomes and reached their minimum levels 33 days after emergence (DAE), the basipetal translocation of photo‐assimilates started earlier (21–23 DAE). The carbon compensation point occurred at eight or six leaves for C. arvense and T. farfara, with a total leaf area of 200 cm2 for both species.
Effects of diets with different protein and dl‐methionine levels on the growth performance and N‐balance of growing minks
Authors: Zhang H. H. , Li G. Y. , Ren E. J. , Xing X. M. , Wu Q. , Yang F. H.
Published: June 2011

This study was performed to evaluate the effects of diets with different protein and dl‐methionine (Met) levels on nitrogen (N) retention, nutrient digestibility, growth performance, and some blood parameters in growing minks. Eighty healthy male minks were selected and randomly divided into five groups with different types of diet. The dietary protein levels, expressed as percentage of dry matter (DM), were 36% (HP) and 28% (LP), corresponding to average 363g and 295g protein/kg DM, respectively. LP was supplemented with Met (0.3%, 0.6% and 0.9% DM); the codes were LP+M1, LP+M2 and LP+M3, respectively. From July to middle of September, the average daily gain and feed: gain ratio (F/G) of the minks that received the diet with 0.6% Met added to the low protein diet was better than feeding HP and other groups. Fecal N and Urinary N of group LP+M2 were the lowest one, in contrast, the daily retention of N was the highest one. Digestibility of DM and CP were not affected by different diets, but digestibility of fat declined with dietary protein level decreasing. Serum urea nitrogen (SUN) was affected by different protein and Met levels. Considering all factors the best performance could be observed offering LP+M2, the prime level of Met was 13.87 g/kg DM in dietary, and 258.5 g digestible protein kg−1 DM was enough for mink in growing period. Furthermore, addition of Met in low protein diets for minks would be beneficial in terms of reduced feed expenses and lower nitrogen emissions to the environment.
Effect of feeding Bacillus subtilis natto fermentation product on milk production and composition, blood metabolites and rumen fermentation in early lactation dairy cows
Authors: Peng H. , Wang J. Q. , Kang H. Y. , Dong S. H. , Sun P. , Bu D. P. , Zhou L. Y.
Published: June 2011

This experiment was conducted to determine the effect of Bacillus subtilis natto fermentation product supplementation on blood metabolites, rumen fermentation and milk production and composition in early lactation dairy cows. Thirty‐six multiparous Holstein cows (DIM = 29 ± 6 days, parity = 2.8 ± 1.1) were blocked by DIM and parity and then randomly assigned to three treatments (12 per treatment) in a 9‐week trial. Cows in control, DFM1 and DFM2 were fed TMR diets supplemented with 0, 6 and 12 g of B. subtilis natto solid‐state fermentation product per day per cow respectively. Plasma non‐esterified fatty acids were lower (p = 0.03) in DFM1 and DFM2 compared with control cows (633 and 639 vs. 685 μm). Ruminal propionate increased (23.9 vs. 26.3 and 26.9/100 mol, control vs. DFM1 and DFM2 respectively) and acetate decreased (64.2 vs. 62.7 and 62.1/100 mol, control vs. DFM1 and DFM2 respectively) with increasing B. subtilis natto fermentation product supplementation. DMI of the cows in three treatments was not affected by B. subtilis natto fermentation product supplementation, but milk yield was 3.1 and 3.2 kg/day higher for DFM1 and DFM2 than that for control cows on average across the 9‐week trial, and significant differences were observed during weeks 5–9 of the trial, which resulted in 9.5% and 11.7% increase in feed efficiency. B. subtilis natto fermentation product supplementation did not affect milk fat percentage and protein yield but increased (p < 0.05) milk fat yield and lactose percentage (p < 0.01) and tended to decrease protein percentage (p = 0.06). The findings show that B. subtilis natto fermentation product was effective in increasing lactation performance of early lactation dairy cows possibly by altering the rumen fermentation pattern without any negative effects on blood metabolites.