II. Yeast sequencing reports. The sequence of 12·5 kb from the right arm of chromosome II predicts a new N-terminal sequence for the IRA1 protein and reveals two new genes,one of which is a DEAD-box helicase

We have determined the complete nucleotide sequence of a 12·5 kb segment from the right arm of chromosome II carried by the cosmid α20. The sequence encodes the 5′ end of the IRA1 gene. Two complete new open reading frames and the 3′ non-coding region of the SUP1 (SUP45) gene. A comparison of our sequence with the data bank reveals a 154 amino acid extension at the N-terminus of Ira1p compared to the previously predicted sequence. According to the 11th edition of the Saccharomyces cerevisiae genetic map, our sequence should encode the MAK5 gene, which is necessary for the maintenance of dsRNA killer plasmids. One of the two new open reading frames, YBR1119, is predicted to encode an RNA helicase, thus YBR1119 may correspond to the MAK5 gene. The sequence has been deposited in the EMBL data library under Accession Number X78937.     

Mapping the 3D-surface strain field of patterned tensile stainless steels using atomic force microscopy

The quantification of microstructural strains at the surface of materials is of major importance for understanding the reactivity of solids. The present paper aims at demonstrating the potentialities of the atomic force microscopy (AFM) for mapping the three-dimensional surface strain field on patterned tensile specimens. Electron beam (e-beam) lithography has been used to deposit 16 x 16 arrays of gold-squared pads. Monitoring the evolution of such a pattern under applied strain allows to quantify the triaxial strains both at the micro-(plastic) domain and nanoscale (elastic) domain vs. applied strain. The proposed method was applied to stainless steels after 4.5% plastic strain.     

Isolation and characterization of a cDNA encoding Arabidopsis thaliana mevalonate kinase by genetic complementation in yeast

A 1.64-kb cDNA encoding an Arabidopsis thaliana mevalonate kinase (MK) was cloned by complementation of the erg 12-1 mutation affecting MK in the yeast Saccharomyces cerevisiae, and the nucleotide sequence was determined. The longest open reading frame encodes a protein of 378 amino acids (aa) with a predicted molecular mass of 40,650 Da. A striking feature of the cDNA sequence is a long 5' untranslated region (322 bp). The deduced aa sequence reveals that the plant enzyme shows strong similarities to the yeast and mammalian enzymes, especially the strong hydrophobicity percentage and several conserved regions. Southern analysis suggests that probably only one locus exists in the A. thaliana genome.     

Analysis of a parallel volume rendering system based on theshear-warp factorization

This paper presents a parallel volume rendering algorithm that can render a 256×256×225 voxel medical data set at over 15 Hz and a 512×512×334 voxel data set at over 7 Hz on a 32-processor Silicon Graphics Challenge. The algorithm achieves these results by minimizing each of the three components of execution time: computation time, synchronization time, and data communication time. Computation time is low because the parallel algorithm is based on the recently-reported shear-warp serial volume rendering algorithm which is over five times faster than previous serial algorithms. The algorithm uses run-length encoding to exploit coherence and an efficient volume traversal to reduce overhead. Synchronization time is minimized by using dynamic load balancing and a task partition that minimizes synchronization events. Data communication costs are low because the algorithm is implemented for shared-memory multiprocessors, a class of machines with hardware support for low-latency fine-grain communication and hardware caching to hide latency. We draw two conclusions from our implementation. First, we find that on shared-memory architectures data redistribution and communication costs do not dominate rendering time. Second, we find that cache locality requirements impose a limit on parallelism in volume rendering algorithms. Specifically, our results indicate that shared-memory machines with hundreds of processors would be useful only for rendering very large data sets     

Functional analysis of Rrp7p, an essential yeast protein involved in pre-rRNA processing and ribosome assembly

During the functional analysis of open reading frames (ORFs) identified during the sequencing of chromosome III of Saccharomyces cerevisiae, the previously uncharacterized ORF YCL031C (now designated RRP7) was deleted. RRP7 is essential for cell viability, and a conditional null allele was therefore constructed, by placing its expression under the control of a regulated GAL promoter. Genetic depletion of Rrp7p inhibited the pre-rRNA processing steps that lead to the production of the 20S pre-rRNA, resulting in reduced synthesis of the 18S rRNA and a reduced ratio of 40S to 60S ribosomal subunits. A screen for multicopy suppressors of the lethality of the GAL::rrp7 allele isolated the two genes encoding a previously unidentified ribosomal protein (r-protein) that is highly homologous to the rat r-protein S27. When present in multiple copies, either gene can suppress the lethality of an RRP7 deletion mutation and can partially restore the ribosomal subunit ratio in Rrp7p-depleted cells. Deletion of both r-protein genes is lethal; deletion of either single gene has an effect on pre-rRNA processing similar to that of Rrp7p depletion. We believe that Rrp7p is required for correct assembly of rpS27 into the preribosomal particle, with the inhibition of pre-rRNA processing appearing as a consequence of this defect.     

Performance of interdigitated nanoelectrodes for electrochemical DNA biosensor

An electrochemical methodology for bio-molecule sensing using an array of well-defined nanostructures is presented. We describe the fabrication by e-beam lithography of nanoelectrodes consisting of a 100 micro m x 50 micro m area containing interdigitated electrodes of 100 nm in width and interelectrode distance of 200 nm. Sensitivity and response time of the nanoelectrodes are compared to the responses of macro- and microelectrodes. The specificity of the sensor is studied by modifying the gold electrodes with DNA. The technique enables to characterize both single and double-stranded DNA of 15 nucleotides. A special electrochemical cell is adapted to control the temperature and measure the DNA concentration by UV analysis. The electrochemical method requires no label on the DNA, only redox mediators were used.     

Influence of iron doping on morphological,structural and optical properties of zinc oxide thin films prepared by dip-coating method

Undoped zinc oxide and iron-doped zinc oxide thin films have been deposited by the sol-geldipcoating method. The Fe/Zn nominal volume ratio was 5% in the solution. The effects of Fe incorporation on morphological, structural, and optical properties of ZnO films were investigated. The scanning electron microscopy measurements showed that the surface morphology of the prepared thin films was affected by Fe doping. The X-ray diffraction patterns of the thin films showed that doped incorporation leads to substantial changes in the structural characteristics of ZnO thin films. The optical absorption measurements indicated a band gap in the range of 3.31 to 3.19 eV. The X-ray photoelectron spectroscopy demonstrated that Fe is incorporated in the ZnO matrix with 6.5 atomic percent (at %). The energy dispersive spectroscopy studies indicated the formation of ZnO with high efficiency.     

HS‐AFM and SERS Analysis of Murine Norovirus Infection: Involvement of the Lipid Rafts

Studies on human norovirus are severely hampered by the absence of a cell culture system until the discovery of murine norovirus (MNV). The cell membrane domains called lipid rafts have been defined as a port of entry for viruses. This study is conducted to investigate murine norovirus binding on the mouse leukemic monocyte macrophage cell line. Lipid raft related structures are extracted from cells by detergent treatment resulting detergent‐resistant membrane (DRMs) domains. The real‐time polymerase chain reaction technique is performed to detect the viral genome, thereby the MNV binding on the DRMs. The interactions between MNV and DRMs are investigated by high‐speed atomic force microscopy (HS‐AFM) combined with surface‐enhanced Raman spectroscopy (SERS). The inoculation of the virus onto cells results in the aggregations of detergent‐resistant membrane domains significantly. The characteristic Raman band of MNV is found in inoculated samples. To be sure that these results are originated from specific interactions between DRM and MNV, methyl‐β‐cyclo‐dextrin (MβCD) is applied to disrupt lipid rafts. The MNV binding on DRMs is precluded by the MβCD treatment. The cholesterols chains are defined as a key factor in the interactions between norovirus and DRMs. The authors conclude that the MNV binding involves the presence of DRMs and cholesterol dependent.     

Preliminary results of the trapped atom clock on a chip

We present an atomic clock based on the interrogation of magnetically trapped ⁸⁷Rb atoms. Two photons, in the microwave and radiofrequency domain, excite the clock transition. At a magnetic field of 3.23 G the clock transition from |F = 1, m_F = -1? to |F = 2, m_F = 1? is 1st-order insensitive to magnetic field variations. Ramsey interrogation times longer than 2 s can be achieved, leading to a projected clock stability in the low 10^-13 at 1 s for a cloud of 10⁵ atoms. We use an atom chip to cool and trap the atoms. A coplanar waveguide is integrated to the chip to carry the Ramsey interrogation signal, making the physics package as small as (5 cm)³. We describe the experimental setup and show preliminary Ramsey fringes of line width 1.25 Hz.     

A family of low and high copy replicative, integrative and single-stranded S. cerevisiae/E. coli shuttle vectors.

We describe a set of replicative, integrative and single-stranded shuttle vectors constructed from the pUC19 plasmid that we use routinely in our experiments. They bear a yeast selectable marker: URA3, TRP1 or LEU2. Replicative vectors carrying different yeast replication origins have been constructed in order to have plasmids based on the same construction with a high or low copy number per cell and with different mitotic stabilities. All the vectors are small in size, provide a high yield in Escherichia coli and efficiently transform Saccharomyces cerevisiae. These plasmids have many of the unique sites of the pUC19 multicloning region and many of them allow for the screening of plasmids with an insert by alpha-complementation. The nucleotide sequence of each of them is completely known.