bluuebunny/crossref_metadata_2025 huggingface dataset:
Opsin activation of transduction in the rods of dark‐reared Rpe65 knockout mice
Authors: Fan Jie , Woodruff Michael L. , Cilluffo Marianne C. , Crouch Rosalie K. , Fain Gordon L.
Published: July 2005

Rpe65 knockout mice (Rpe65−/−) are unable to synthesize the visual pigment chromophore 11‐cis retinal; however, if these animals are reared in complete darkness, the rod photoreceptors accumulate a small amount of 9‐cis retinal and its corresponding visual pigment isorhodopsin. Suction‐electrode recording of single rods from dark‐reared Rpe65−/− mice showed that the rods were about 400 times less sensitive than wild‐type control rods and that the maximum responses were much smaller in amplitude. Spectral sensitivity measurements indicated that Rpe65−/− rod responses were generated by isorhodopsin rather than rhodopsin. Sensitivity and pigment concentration were compared in the same mice by measuring light responses from rods of one eye and pigment concentration from the retina of the other eye. Retinas had 11–35% of the normal pigment level, but the rods were of the order of 20–30 times less sensitive than could be accounted for by the loss in quantum catch. This extra desensitization must be caused by opsin‐dependent activation of the visual cascade, which leads to a state equivalent to light adaptation in the dark‐adapted rod. By comparing the sensitivity of dark‐reared Rpe65−/− rods to that produced in normal rods by background light, we estimate that Rpe65−/− opsin is of the order of 2.5 × 10−5 as efficient in activating transduction as photoactivated rhodopsin (Rh*) in WT mice. Dark‐reared Rpe65−/− rods are less desensitized than rods from cyclic light‐reared Rpe65−/− mice, have about 50% more photocurrent and degenerate at a slower rate. Retinas sectioned after 9 months in darkness show a larger number of photoreceptor nuclei in dark‐reared animals than in cyclic light‐reared animals, though both have fewer nuclei than in cyclic light‐reared wild‐type retinas. Both also have shorter outer segments and a lower free‐Ca2+ concentration. These experiments provide the first quantitative measurement of opsin activation in physiologically responding mammalian rods.
Ubiquitination on Nonlysine Residues by a Viral E3 Ubiquitin Ligase
Authors: Cadwell Ken , Coscoy Laurent
Published: July 2005

Ubiquitination controls a broad range of cellular functions. The last step of the ubiquitination pathway is regulated by enzyme type 3 (E3) ubiquitin ligases. E3 enzymes are responsible for substrate specificity and catalyze the formation of an isopeptide bond between a lysine residue of the substrate (or the N terminus of the substrate) and ubiquitin. MIR1 and MIR2 are two E3 ubiquitin ligases encoded by Kaposi's sarcoma–associated herpesvirus that mediate the ubiquitination of major histocompatibility complex class I (MHC I) molecules and subsequent internalization. Here, we found that MIR1, but not MIR2, promoted down-regulation of MHC I molecules lacking lysine residues in their intracytoplasmic domain. In the presence of MIR1, these MHC I molecules were ubiquitinated, and their association with ubiquitin was sensitive to β
2
-mercaptoethanol, unlike lysine-ubiquitin bonds. This form of ubiquitination required a cysteine residue in the intracytoplasmic tail of MHC I molecules. An MHC I molecule containing a single cysteine residue in an artificial glycine and alanine intracytoplasmic domain was endocytosed and degraded in the presence of MIR1. Thus, ubiquitination can occur on proteins lacking accessible lysines or an accessible N terminus.
Addition of Poly(A) and Heteropolymeric 3′ Ends inBacillus subtilisWild-Type and Polynucleotide Phosphorylase-Deficient Strains
Authors: Campos-Guillén Juan , Bralley Patricia , Jones George H. , Bechhofer David H. , Olmedo-Alvarez Gabriela
Published: July 2005

Polyadenylation plays a role in decay of some bacterial mRNAs, as well as in the quality control of stable RNA. InEscherichia coli, poly(A) polymerase I (PAP I) is the main polyadenylating enzyme, but the addition of 3′ tails also occurs in the absence of PAP I via the synthetic activity of polynucleotide phosphorylase (PNPase). The nature of 3′-tail addition inBacillus subtilis, which lacks an identifiable PAP I homologue, was studied. Sizing of poly(A) sequences revealed a similar pattern in wild-type and PNPase-deficient strains. Sequencing of 152 cloned cDNAs, representing 3′-end sequences of nontranslated and translated RNAs, revealed modified ends mostly on incomplete transcripts, which are likely to be decay intermediates. The 3′-end additions consisted of either short poly(A) sequences or longer heteropolymeric ends with a mean size of about 40 nucleotides. Interestingly, multiple independent clones exhibited complex heteropolymeric ends of very similar but not identical nucleotide sequences. Similar polyadenylated and heteropolymeric ends were observed at 3′ ends of RNA isolated from wild-type andpnpAmutant strains. These data demonstrated that, unlike the case of some other bacterial species and chloroplasts, PNPase ofBacillus subtilisis not the major enzyme responsible for the addition of nucleotides to RNA 3′ ends.
The IncP-6 Plasmid Rms149 Consists of a Small Mobilizable Backbone with Multiple Large Insertions
Authors: Haines Anthony S. , Jones Karen , Cheung Martin , Thomas Christopher M.
Published: July 2005

Plasmid Rms149, the archetype ofPseudomonasplasmid incompatibility group IncP-6, was identified inPseudomonas aeruginosaas an agent conferring resistance to streptomycin, sulfanilamide, gentamicin, and carbenicillin in 1975. It has been classed as a broad-host-range plasmid due to its ability to replicate in bothEscherichia coli(where it is designated IncG) andPseudomonasspecies, although both species are γ-proteobacteria. To provide reference information on this Inc group, we have determined the complete sequence of Rms149 and found that, although the genome comprises 57,121 bp, it is essentially a small mobilizable plasmid carrying multiple mobile elements, which make up 79% (>45 kb) of its genome. A replicon has been identified which encodes a single polypeptide with moderate identity to other replication proteins. The region encoding this protein can replicate inPseudomonas putidaandE. coli. This sequence is directly downstream of a putative partitioning region highly similar to that of pRA2. A functional IncQ-type mobilization region is also present. Thus, the backbone appears to be a novel combination of modules already identified in other plasmid systems. Analysis of the segments that fall outside this core of stable inheritance and transfer functions show that this plasmid has been subject to multiple insertion events and that the plasmid appears to carry a considerable load of DNA that no longer should be phenotypically advantageous. The plasmid therefore functions not just as a vehicle for spread of selective traits but also as a store for DNA that is not currently under selection.
Chill Activation of Compatible Solute Transporters in
Corynebacterium glutamicum
at the Level of Transport Activity
Authors: Özcan Nuran , Krämer Reinhard , Morbach Susanne
Published: July 2005

The gram-positive soil bacterium
Corynebacterium glutamicum
harbors four osmoregulated secondary uptake systems for compatible solutes, BetP, EctP, LcoP, and ProP. When reconstituted in proteoliposomes, BetP was shown to sense hyperosmotic conditions via the increase in luminal K
+
and to respond by instant activation. To study further putative ways of stimulus perception and signal transduction, we have investigated the responses of EctP, LcoP, and BetP, all belonging to the betaine-carnitine-choline transporter family, to chill stress at the level of activity. When fully activated by hyperosmotic stress, they showed the expected increase of activity at increasing temperature. In the absence of osmotic stress, EctP was not activated by chill and LcoP to only a very low extent, whereas BetP was significantly stimulated at low temperature. BetP was maximally activated at 10°C, reaching the same transport rate as that observed under hyperosmotic conditions at this temperature. A role of cytoplasmic K
+
in chill-dependent activation of BetP was ruled out, since (i) the cytoplasmic K
+
concentration did not change significantly at lower temperatures and (ii) a mutant BetP lacking the C-terminal 25 amino acids, which was previously shown to have lost the ability to be activated by luminal K
+
, was fully competent in chill sensing. When heterologously expressed in
Escherichia coli
, BetP did not respond to chill stress. This may indicate that the membrane in which BetP is inserted plays an important role in chill activation and thus in signal transduction by BetP, different from the previously established K
+
-mediated process.
Mutations in the C-Terminal Region of TraM Provide Evidence for In Vivo TraM-TraD Interactions during F-Plasmid Conjugation
Authors: Lu Jun , Frost Laura S.
Published: July 2005

Conjugation is a major mechanism for disseminating genetic information in bacterial populations, but the signal that triggers it is poorly understood in gram-negative bacteria. F-plasmid-mediated conjugation requires TraM, a homotetramer, which binds cooperatively to three binding sites within the origin of transfer. Using in vitro assays, TraM has previously been shown to interact with the coupling protein TraD. Here we present evidence that F conjugation also requires TraM-TraD interactions in vivo. A three-plasmid system was used to select mutations in TraM that are defective for F conjugation but competent for tetramerization and cooperative DNA binding to thetraMpromoter region. One mutation, K99E, was particularly defective in conjugation and was further characterized by affinity chromatography and coimmunoprecipitation assays that suggested it was defective in interacting with TraD. A C-terminal deletion (S79*, where the asterisk represents a stop codon) and a missense mutation (F121S), which affects tetramerization, also reduced the affinity of TraM for TraD. We propose that the C-terminal region of TraM interacts with TraD, whereas its N-terminal domain is involved in DNA binding. This arrangement of functional domains could in part allow TraM to receive the mating signal generated by donor-recipient contact and transfer it to the relaxosome, thereby triggering DNA transfer.
Transcription Analysis of the Major Antigenic Protein 1 Multigene Family of Three In Vitro-Cultured
Ehrlichia ruminantium
Isolates
Authors: Bekker Cornelis P. J. , Postigo Milagros , Taoufik Amar , Bell-Sakyi Lesley , Ferraz Conchita , Martinez Dominique , Jongejan Frans
Published: July 2005

Ehrlichia ruminantium
, an obligate intracellular bacterium transmitted by ticks of the genus
Amblyomma
, causes heartwater disease in ruminants. The gene coding for the major antigenic protein MAP1 is part of a multigene family consisting of a cluster containing 16 paralogs. In the search for differentially regulated genes between
E. ruminantium
grown in endothelial and tick cell lines that could be used in vaccine development and to determine if differences in the
map1
gene cluster exist between different isolates of
E. ruminantium
, we analyzed the
map1
gene cluster of the Senegal and Gardel isolates of
E. ruminantium
. Both isolates contained the same number of genes, and the same organization as found in the genome sequence of the Welgevonden isolate (H. Van Heerden, N. E. Collins, K. A. Brayton, C. Rademeyer, and B. A. Allsopp, Gene
330:
159-168, 2004). However, comparison of two subpopulations of the Gardel isolate maintained in different laboratories demonstrated that recombination between
map1
-
3
and
map1
-
2
had occurred in one subpopulation with deletion of one entire gene. Reverse transcription-PCR on
E. ruminantium
derived mRNA from infected cells using gene-specific primers revealed that all 16
map1
paralogs were transcribed in endothelial cells. In one vector (
Amblyomma variegatum
) and several nonvector tick cell lines infected with
E. ruminantium
, transcripts were found for between 4 and 11 paralogs. In all these cases the transcript for the
map1
-
1
gene was detected and was predominant. Our results indicate that the
map1
gene cluster is relatively conserved but can be subject to recombination, and differences in the transcription of
map1
multigenes in host and vector cell environments exist.
Enhancement of Glutamine Utilization in
Bacillus subtilis
through the GlnK-GlnL Two-Component Regulatory System
Authors: Satomura Takenori , Shimura Daisuke , Asai Kei , Sadaie Yoshito , Hirooka Kazutake , Fujita Yasutaro
Published: July 2005

During DNA microarray analysis, we discovered that the GlnK-GlnL (formerly YcbA-YcbB) two-component system positively regulates the expression of the
glsA-glnT
(formerly
ybgJ-ybgH
) operon in response to glutamine in the culture medium on Northern analysis. As a result of gel retardation and DNase I footprinting analyses, we found that the GlnL protein interacts with a region (bases −13 to −56; +1 is the transcription initiation base determined on primer extension analysis of
glsA
-
glnT
) in which a direct repeat, TTTTGTN4TTTTGT, is present. Furthermore, the
glsA
and
glnT
genes were biochemically verified to encode glutaminase and glutamine transporter, respectively.
Low-Molecular-Weight Protein Tyrosine Phosphatases ofBacillus subtilis
Authors: Musumeci Lucia , Bongiorni Cristina , Tautz Lutz , Edwards Robert A. , Osterman Andrei , Perego Marta , Mustelin Tomas , Bottini Nunzio
Published: July 2005

In gram-negative organisms, enzymes belonging to the low-molecular-weight protein tyrosine phosphatase (LMPTP) family are involved in the regulation of important physiological functions, including stress resistance and synthesis of the polysaccharide capsule. LMPTPs have been identified also in gram-positive bacteria, but their functions in these organisms are presently unknown. We cloned two putative LMPTPs fromBacillus subtilis, YfkJ and YwlE, which are highly similar to each other in primary structure as well as to LMPTPs from gram-negative bacteria. When purified from overexpressingEscherichia colistrains, both enzymes were able to dephosphorylatep-nitrophenyl-phosphate and phosphotyrosine-containing substrates in vitro but showed significant differences in kinetic parameters and sensitivity to inhibitors. Transcriptional analyses showed thatyfkJwas transcribed at a low level throughout the growth cycle and underwent a σB-dependent transcriptional upregulation in response to ethanol stress. The transcription ofywlEwas growth dependent but stress insensitive. Genomic deletion of each phosphatase-encoding gene led to a phenotype of reduced bacterial resistance to ethanol stress, which was more marked in theywlEdeletion strain. Our study suggests that YfkJ and YwlE play roles inB. subtilisstress resistance.
Crystal Structure of an Iron-Dependent Group III Dehydrogenase That Interconvertsl-Lactaldehyde andl-1,2-Propanediol inEscherichia coli
Authors: Montella Cristina , Bellsolell Lluis , Pérez-Luque Rosa , Badía Josefa , Baldoma Laura , Coll Miquel , Aguilar Juan
Published: July 2005

The FucO protein, a member of the group III “iron-activated” dehydrogenases, catalyzes the interconversion betweenl-lactaldehyde andl-1,2-propanediol inEscherichia coli. The three-dimensional structure of FucO in a complex with NAD+was solved, and the presence of iron in the crystals was confirmed by X-ray fluorescence. The FucO structure presented here is the first structure for a member of the group III bacterial dehydrogenases shown experimentally to contain iron. FucO forms a dimer, in which each monomer folds into an α/β dinucleotide-binding N-terminal domain and an all-α-helix C-terminal domain that are separated by a deep cleft. The dimer is formed by the swapping (between monomers) of the first chain of the β-sheet. The binding site for Fe2+is located at the face of the cleft formed by the C-terminal domain, where the metal ion is tetrahedrally coordinated by three histidine residues (His200, His263, and His277) and an aspartate residue (Asp196). The glycine-rich turn formed by residues 96 to 98 and the following α-helix is part of the NAD+recognition locus common in dehydrogenases. Site-directed mutagenesis and enzyme kinetic assays were performed to assess the role of different residues in metal, cofactor, and substrate binding. In contrast to previous assumptions, the essential His267 residue does not interact with the metal ion. Asp39 appears to be the key residue for discriminating against NADP+. Modelingl-1,2-propanediol in the active center resulted in a close approach of the C-1 hydroxyl of the substrate to C-4 of the nicotinamide ring, implying that there is a typical metal-dependent dehydrogenation catalytic mechanism.
PhoR1-PhoP1, a Third Two-Component System of the Family PhoRP from
Myxococcus xanthus
: Role in Development
Authors: Carrero-Lérida Juana , Moraleda-Muñoz Aurelio , García-Hernández Raquel , Pérez Juana , Muñoz-Dorado José
Published: July 2005

The pair PhoR1-PhoP1 is the third two-component system of the family PhoRP reported in
M. xanthus
. PhoR1 is a histidine kinase anchored to the membrane through a transmembrane domain located in the amino-terminal portion of the protein. As a result, 93% of the protein is located in the cytoplasm. This topology is unusual in the PhoR-type histidine kinases. PhoP1 is a response regulator with a helix-loop-helix motif typical of the DNA-binding proteins. Although the operon
phoPR1
is expressed during vegetative growth, it peaks during development. The expression levels of this operon are higher in phosphate-containing media than in those in which the nutrient is absent. A deletion mutant in this system exhibits a delay in aggregation and the formation of fruiting bodies larger than those of the wild-type strain. The expression of the operon is autoregulated. This system is also partially responsible for the expression of Mg-independent acid and neutral phosphatases, but it is not required for the expression of alkaline phosphatases.
Extrachromosomal DNA of the SymbiontSodalis glossinidius
Authors: Darby A. C. , Lagnel J. , Matthew C. Z. , Bourtzis K. , Maudlin I. , Welburn S. C.
Published: July 2005

The extrachromosomal DNA ofSodalis glossinidiusfrom two tsetse fly species was sequenced and contained four circular elements: three plasmids, pSG1 (82 kb), pSG2 (27 kb), and pSG4 (11 kb), and a bacteriophage-like pSG3 (19 kb) element. The information suggestsS. glossinidiusis evolving towards an obligate association with tsetse flies.
Functional and Topological Analysis of the
Burkholderia cenocepacia
Priming Glucosyltransferase BceB, Involved in the Biosynthesis of the Cepacian Exopolysaccharide
Authors: Videira Paula A. , Garcia Abbner P. , Sá-Correia Isabel
Published: July 2005

The BceB protein of the cystic fibrosis mucoid isolate
Burkholderia cenocepacia
IST432 is proposed to catalyze the first step of the exopolysaccharide repeat unit assembly. Extracts of
Escherichia coli
cells overexpressing BceB were shown to contain glycosyltransferase activity and mediate incorporation of glucose-1-phosphate into membrane lipids. The amino acid sequence of BceB exhibits two conserved regions, one comprising two invariant aspartic acid residues (Asp339 and Asp355) that are essential for catalysis, as substantiated by site-directed mutagenesis, and the other comprising a putative Rossmann fold motif. The results of protein topology analysis using PhoA and LacZ fusions supported in silico predictions that BceB has at least six transmembrane segments and two major cytoplasmic loops comprising the conserved regions described above.
The Gene Encoding the Glutamate Dehydrogenase in
Lactococcus lactis
Is Part of a Remnant Tn
3
Transposon Carried by a Large Plasmid
Authors: Tanous Catherine , Chambellon Emilie , Sepulchre Anne-Marie , Yvon Mireille
Published: July 2005

The gene responsible for the uncommon glutamate dehydrogenase (GDH) activity of
Lactococcus lactis
was identified and characterized. It encodes a GDH of family I that is mainly active in glutamate biosynthesis, is carried by a large plasmid, and is included, with functional cadmium resistance genes, in a remnant Tn
3
-like transposon.
EspC Is Involved in Controlling the Timing of Development in
Myxococcus xanthus
Authors: Lee Bongsoo , Higgs Penelope I. , Zusman David R. , Cho Kyungyun
Published: July 2005

The
espC
null mutation caused accelerated aggregation and formation of tiny fruiting bodies surrounded by spores, which were also observed in the
espA
mutant and in CsgA-overproducing cells in
Myxococcus xanthus
. In addition, the
espC
mutant appeared to produce larger amounts of the complementary C-signal than the wild-type strain. These findings suggest that EspC is involved in controlling the timing of fruiting body development in
M. xanthus.
Identification of
nlmTE
, the Locus Encoding the ABC Transport System Required for Export of Nonlantibiotic Mutacins in
Streptococcus mutans
Authors: Hale John D. F. , Heng Nicholas C. K. , Jack Ralph W. , Tagg John R.
Published: July 2005

Streptococcus mutans
UA159, the genome sequence reference strain, exhibits nonlantibiotic bacteriocin (mutacin) activity. In this study, we have combined bioinformatic and mutational analyses to identify the ABC transporter designated NlmTE, which is required for mutacin biogenesis in strain UA159 as well as in another mutacin producer,
S. mutans
N.
Equine Infectious Anemia Virus Gag p9 Function in Early Steps of Virus Infection and Provirus Production
Authors: Jin Sha , Chen Chaoping , Montelaro Ronald C.
Published: July 2005

We have previously reported that serial truncation of the Gag p9 protein of equine infectious anemia virus (EIAV) revealed a progressive loss in replication phenotypes in transfected cells, such that a proviral mutant (E32) expressing the N-terminal 31 amino acids of p9 produced infectious virus particles similarly to parental provirus, while a proviral mutant (K30) with two fewer amino acids produced replication-defective virus particles, despite containing apparently normal levels of processed Gag and Pol proteins (C. Chen, F. Li, and R. C. Montelaro, J. Virol.
75:
9762-9760, 2001). Based on these observations, we sought in the current study to identify the precise defect in K30 virion infection of permissive equine dermal (ED) cells. The results of these experiments clearly demonstrated that K30 virions entered target ED cells and produced early (minus-strand strong-stop) and late (Gag) viral DNA products as efficiently as did the replication-competent E32 mutant and parental EIAV
UK
viruses. However, in contrast to the replication-competent E32 mutant and parental viruses, infection with K30 mutant virus failed to produce detectable two-long-terminal-repeat DNA circles, stable integrated provirus, virus-specific Gag mRNA expression, or intracellular viral protein expression. Taken together, these data demonstrate that the K30 mutant is defective in the ability to produce sufficient nuclear viral DNA to establish a productive infection in ED cells. Thus, these observations indicate for the first time that the EIAV Gag p9 protein performs a critical role in viral DNA production and processing to provirus during EIAV infection, in addition to its previously defined role in viral budding mediated by the p9 L domain.
Plant Virus HC-Pro Is a Determinant of Eriophyid Mite Transmission
Authors: Stenger Drake C. , Hein Gary L. , Gildow Frederick E. , Horken Kempton M. , French Roy
Published: July 2005

The eriophyid mite transmittedWheat streak mosaic virus(WSMV; genusTritimovirus, familyPotyviridae) shares a common genome organization with aphid transmitted species of the genusPotyvirus. Although both tritimoviruses and potyviruses encode helper component-proteinase (HC-Pro) homologues (required for nonpersistent aphid transmission of potyviruses), sequence conservation is low (amino acid identity, ∼16%), and a role for HC-Pro in semipersistent transmission of WSMV by the wheat curl mite (Aceria tosichella[Keifer]) has not been investigated. Wheat curl mite transmissibility was abolished by replacement of WSMV HC-Pro with homologues of an aphid transmitted potyvirus (Turnip mosaic virus), a rymovirus (Agropyron mosaic virus) vectored by a different eriophyid mite, or a closely related tritimovirus (Oat necrotic mottle virus; ONMV) with no known vector. In contrast, both WSMV-Sidney 81 and a chimeric WSMV genome bearing HC-Pro of a divergent strain (WSMV-El Batán 3; 86% amino acid sequence identity) were efficiently transmitted byA. tosichella. Replacing portions of WSMV-Sidney 81 HC-Pro with the corresponding regions from ONMV showed that determinants of wheat curl mite transmission map to the 5′-proximal half of HC-Pro. WSMV genomes bearing HC-Pro of heterologous species retained the ability to form virions, indicating that loss of vector transmissibility was not a result of failure to encapsidate. Although titer in systemically infected leaves was reduced for all chimeric genomes relative to WSMV-Sidney 81, titer was not correlated with loss of vector transmissibility. Collectively, these results demonstrate for the first time that HC-Pro is required for virus transmission by a vector other than aphids.
Essential and Nonessential Elements in the 3′ Nontranslated Region of Bovine Viral Diarrhea Virus
Authors: Pankraz Alexander , Thiel Heinz-Jürgen , Becher Paul
Published: July 2005

The 3′ nontranslated region (NTR) of the pestivirus
Bovine viral diarrhea virus
(BVDV), a close relative of human
Hepatitis C virus
, consists of three stem-loops which are separated by two single-stranded regions. As in other positive-stranded RNA viruses, the 3′ NTR of pestiviruses is involved in crucial processes of the viral life cycle. While several studies characterized
cis
-acting elements within the 3′ NTR of a BVDV replicon, there are no studies addressing the significance of these elements in the context of a replicating virus. To examine the functional importance of 3′ NTR elements, a set of 4-base deletions and deletions of each of the three stem-loops were introduced into an infectious BVDV cDNA clone. Emerging mutant viruses were characterized with regard to plaque phenotype, growth kinetics, and synthesis of viral RNA. The results indicated that presence of stem-loop (SL) I and the 3′-terminal part of the single-stranded region between stem-loops I and II are indispensable for pestiviral replication. In contrast, deletions within SL II and SL III as well as absence of either SL II or SL III still allowed efficient viral replication; however, a mutant RNA lacking both SL II and SL III was not infectious. The results of this study provide a detailed map of the essential and nonessential elements within the 3′ NTR of BVDV and contribute to our understanding of sequence and structural elements important for efficient viral replication of pestiviruses in natural host cells.
A REVIEW OF PERFORMANCE EVALUATION FOR BIOMETRICS SYSTEMS
Authors: HONG JIN-HYUK , YUN EUN-KYUNG , CHO SUNG-BAE
Published: July 2005

Biometrics is a technology designed to automatically recognize a person together with his/her natural and distinct characteristics. Recently it is in the limelight as an effective authentication method of information. With the great interests in biometrics, the need for reliable evaluation of these technologies increases and the research on objective and quantitative performance estimation methodology is actively investigated. In this paper, we give a comprehensive overview of biometric technology and performance evaluation with more than 100 publications, specially focused on fingerprints. After the thorough review, we propose a promising evaluation method based on affecting factors.
3D STRUCTURE AND MOTION ESTIMATION FROM RANGE AND INTENSITY IMAGES USING PARTICLE FILTERING
Authors: NOYER JEAN-CHARLES , BOUCHER CHRISTOPHE , BENJELLOUN MOHAMMED
Published: July 2005

This article deals with an estimation method of 3D structure and motion. The object is described by line segments and points assuming that it can be described by a polygonal model. It models the problem which is solved by a nonlinear estimation method: The Particle Filter. This method can account for nonlinear models and non-Gaussian statistics without any linearization stage like the Extended Kalman Filter (EKF), for example. The increase in accuracy is shown on a vision system composed by sensors delivering range and intensity/reflectance image sequences. Finally, the solution is compared with a commonly used state estimation method (EKF).
COMPUTATIONAL STUDIES OF THE AMMONOLYSIS FOR N-METHYL β-SULTAM
Authors: HE MAOXIA , FENG DACHENG , XIE JU , CAI ZHENGTING
Published: July 2005

As a first step toward the understanding of the aminolysis reaction of β-sultam compounds, the ammonolysis and the effect of a second ammonia on the ammonolysis reactions of N -methyl β-sultam have been studied using Density Functional Theory (DFT) method at the B3LYP/6-31G* level. The exploration of the reaction processes proposed two different mechanisms: concerted and stepwise mechanisms. There is one pathway in concerted mechanism and two pathways in stepwise mechanisms: pathways a and b. The calculations of reaction energy barriers show that the nonconcerted route is the more favored one. Solvent effects were assessed by the PCM method. The results show that the pathway a in channel II is the most favorable in both cases. The presence of solvent disfavors the reaction, and the participation of ammonia in the ammonolysis reaction plays a positive role and reduces the active energy greatly. All transition states in the assisted ammonolysis are 45–65 kJ/mol lower than those for the non-assisted reaction. The results also show that the ammonolysis reaction have a higher energy barrier than the alcoholysis reaction. This low reactivity of amines is also observed in the reactions of N -benzoyl β-sultam and p-nitrophenyl toluene-p-sulfonate where there is a distinct preference towards oxygen nucleophiles.
THEORETICAL STUDY ON THE MECHANISM OF THE REACTION OF Ni(d10 1S) + H2 + CO2 → NiCO + H2O
Authors: QIN SONG , HU CHANGWEI , YANG HUAQING
Published: July 2005

The detailed singlet potential energy surface (PES) of the reaction of Ni ( d 10 1 S ) + H 2 + CO 2→ NiCO + H2O is investigated at the CCSD(T) /6-311+ G(2d,2p) // B3LYP /6-311+ G(2d,2p) levels in order to explore possible reaction mechanism of CO 2 hydrogenation on Ni center. The calculation predicts that the co-interacted H 2 involved C–O bond cleavage of CO 2 molecule is prior to the dissociation of adsorbed H 2 molecule, and the entire reaction is exothermic by 297.3 kJ/mol with an energy barrier of 137.7 kJ/mol. The rate-determining step (RDS) for the overall reaction is predicted to be the insertion of Ni into the C–O bond of the CO 2 moiety.
PREDICTION OF THE ENTHALPY OF FORMATION OF HALOGENATED HYDROCARBONS USING SPARC
Authors: WHITESIDE TAD S. , CARREIRA LIONEL A.
Published: July 2005

Standard enthalpies of formation of halogenated hydrocarbons were calculated from models developed for the computer program SPARC. SPARC uses computational algorithms based on chemical structure theory to calculate molecular properties. Molecular structures are broken into simple functional units (reactophores) with intrinsic properties. Each reactophore is analyzed and the effects of appended molecular structures are quantified through perturbation theory. The halohydrocarbons modeled include multi-branched chains, simple conjugated rings, and aromatic compounds. SPARC calculates an RMS deviation of 5.18 kJ mol-1 for these 202 compounds.
Evidence of Correlation between Dark Spots and Dislocations Originating from Substrate in Light-Emitting Diodes
Authors: Hobo Kenji , Sone Hidetoshi , Kato Toshihiro , Hirotani Masumi , Saka Takashi
Published: July 2005

Light-emitting diodes were fabricated with 150-µm-diameter emitting windows. Multi-epitaxial layers were grown by the metalorganic chemical vapor deposition method. The diodes contained a GaAs active layer and a distributed Bragg reflector. Multiple defects were observed on the surfaces of the epitaxial layers. The distributions of the defects were compared with the dislocation distributions of the substrates revealed by the conventional etching method. Since the distributions of both were similar, the defects are considered to be due to dislocations that are present in the substrates. The dislocations threaded through the distributed Bragg reflector and the epitaxial layers during growth. After operation for 2 h with forward currents of 100 mA, dark spots appeared at the positions where the defects were observed. Therefore, it is concluded that the dislocations act as non-radiative centers causing dark spots and device degradation.
Preparation and Optical Properties of Zirconium–Titanium–Oxide Thin Films by Reactive Sputtering
Authors: Matsumoto Hironaga , Sekine Masato , Miura Noboru , Nakano Ryotaro , Matsumoto Setsuko
Published: July 2005

Zirconium–titanium–oxide thin films were prepared by multi-target rf reactive sputtering using metallic targets of zirconium and titanium. The compositional ratio of zirconium to titanium in the thin films was precisely controlled through rf power. Zirconium and titanium in the thin films were found to exist as mixtures of chemically bonded ZrO2 and TiO2 from XPS spectra. The zirconium–titanium–oxide thin films with compositional ratio x<0.42 were identified to have a tetragonal crystal structure, whereas those with x≧0.42 were identified to be in the amorphous state. The refractive index of the zirconium–titanium–oxide thin film at a wavelength of 550 nm changed from 2.25 to 2.55 according to compositional ratio x, and the dispersion of the refractive index was analyzed using the Lorentz oscillator model with four oscillators. It was clarified that the estimated oscillator energies E
1 (10.5 eV) and E
2 (6.5 eV) correspond to zirconium oxide, and that E
3 (5.5 eV) and E
4 (4.3 eV) correspond to titanium oxide from fundamental absorption spectra and photoconductivity.
Analysis of the Photochemical Reaction on the Surface for Room Temperature Deposition of SiO2 Thin Films by Photo-CVD using Vacuum Ultraviolet Light
Authors: Yokotani Atsushi , Amari Kouichi , Maezono Yoshinari , Toshikawa Kiyohiko , Kurosawa Kou
Published: July 2005

We have analyzed the photochemical reaction for the deposition of SiO2 thin films at room temperature in photo-CVD using a vacuum ultraviolet (VUV) excimer lamp with reflection-absorption spectroscopy using a Fourier transform infrared spectrometer (RAS-FTIR). Tetraethoxyorthosilicate (TEOS) was used as a precursor and two types of excimer lamps were used as light sources. The reaction in VUV-CVD is divided into two stages: the reaction in the vapor phase, and the reaction on the surface of the substrate. In this work, we analyzed the latter stage. As a result of analyzing the spectra obtained, it was found that the main reaction for the formation of the SiO2 film was in the latter stage, in which the dissociation of Si–O bonds in Si–O–CH2 in the adsorbed fragments was preceded by the photo-dissociation of C2H5.
Effect of Post-Metallization Annealing on Electrical Characteristics of La2O3 Gate Thin Films
Authors: Kuriyama Atsushi , Ohmi Shun-ichiro , Tsutsui Kazuo , Iwai Hiroshi
Published: July 2005

Annealing conditions of a lanthanum oxide (La2O3) metal–insulator–semiconductor (MIS) capacitor were studied in order to optimize the flat-band voltage (V
FB). It was confirmed that in the case of using Al electrodes, negative V
FB shift was increased by post-deposition annealing (PDA) (before metallization) compared to as-deposited sample, while all other characteristics, such as EOT, leakage current and interface state density, were improved. It was also confirmed that post-metallization annealing (PMA) suppressed the V
FB shift. Finally, the combination of PDA and PMA resulted in the recovery of V
FB shift with suppression of the decrease of EOT. However, it was confirmed that in the case of using Au electrodes, PMA resulted in a slight negative V
FB shift. Judging from these results, it is conceivable that the reaction of the metal with La2O3 exerts a significant influence on the V
FB shift.
Growth Processes and Control of Two-Dimensional Structure of Carboxylic Acid-Terminated Self-Assembled Monolayers on Au(111)
Authors: Noh Jaegeun , Konno Kaoru , Ito Eisuke , Hara Masahiko
Published: July 2005

The growth processes and solvent effects on the two-dimensional structure of self-assembled monolayers (SAMs) formed by 6-mercaptohexanoic acid (MHA) on Au(111) were examined by scanning tunneling microscopy (STM) and contact angle (CA) measurements. The STM study revealed for the first time that the striped phases of 6-mercaptohexanoic acid (MHA) on Au(111) are preferentially formed near the step edges of gold terraces in the initial stage of SAM growth. In addition, it was found that MHA SAMs prepared from a polar aprotic solvent form a more well-ordered structure and a better hydrophilic surface than those prepared from a polar protic solvent. From this study, we clearly demonstrated that the properties of solvents are very important factors in controlling the two-dimensional structure of carboxylic acid-terminated SAMs.
Effect of Pulse-Reverse Current on Microstructure and Properties of Electroformed Nickel–Iron Mold Insert
Authors: Yeh Yih-Min , Chen Chin-Sung , Tsai Ming-Hung , Shyng Yih-Chuen , Lee Sheng-Yang , Ou Keng-Liang
Published: July 2005

A high-technology approach to the manufacture of microdevices and Ni–Fe films formed by electroforming processes was investigated. The properties of Ni–Fe films were evaluated by stress measurement, transmission electron microscopy (TEM), scanning probe microscopy (SPM) and nanoindentation analysis. Square-wave cathodic current modulation was employed to electrodeposit ultrafine-grained Ni–Fe films from an additive-free Watts bath. The effects of pulse parameters, namely, pulse on-time, pulse off-time and peak-current density on grain size, surface morphology and crystal orientation were determined. Current density significantly influences the microstructure of what. Increasing current density substantially refined the deposited crystals. The crystal size of Ni–Fe films decreased as current density increased. Microstructural modification was accompanied by the corresponding variations in microhardness, current efficiency and hydrogen content. These results are explained by the strong tendency of Ni–Fe to be passivated though the adsorption of foreign species (hydrogen and hydroxide) present during crystallization. However, increasing current density did not affect crystal orientation, indicating that a high pulse-reverse current density inhibits the adsorption of hydrogen species onto Ni–Fe films. Therefore, Ni–Fe films have a low internal stress and a low surface roughness. Current density considerably influences the microstructure of what, revealing that a high pulse-reversed current density inhibits the adsorption of hydrogen species onto Ni–Fe deposits, so that an as-deposited pulse-reversed Ni–Fe alloy has a lower internal stress and a lower surface roughness than a Ni–Fe alloy deposited by direct current density.
Novel and Practical Gap Measurement Method for Reflective Liquid Crystal Cells
Authors: Nishioka Takahiro , Satake Tetsuya , Kurata Tetsuyuki , Maehara Toshiaki
Published: July 2005

We have developed a novel gap measurement method called the “Advanced reflection analysis (AREA)” method, which is based on the analysis of the intensity of the reflected light from a reflective liquid crystal cell. By taking account of the anisotropy of the optical property of a half-mirror and reflected light from a cell surface, an accurate microscopic measurement of cell gap can be realized using a reflective polarization microscope.
Index Profile of Radial Gradient Index Lens Measured by Imaging Ellipsometric Technique
Authors: Chao Yu Faye , Lee Kan Yan
Published: July 2005

A simple three-intensity imaging ellipsometric technique is proposed for measurement of the refractive index profile (RIP) of a radial gradient index (GRIN) lens. According to our numerical analysis, the improved ellipsometric parameters measured by this method are valid as long as the azimuth deviation of the polarizer is less than 3°. A BK7 glass and a radial GRIN lens were measured. A fairly flat refractive index surface profile was obtained for the glass within a 0.3% error. The on-axis refractive index of the radial GRIN lens and its RIP are well fitted to the specifications provided by the manufacturer. Instead of the refracted-ray method, we provide a reflective and nondestructive measurement technique for measurement of the gradient index of a flat surface.
Dry Etching of Cr2O3/Cr Stacked Film during Resist Ashing by Oxygen Plasma
Authors: Tonotani Junichi , Ohmi Shun-ichiro , Iwai Hiroshi
Published: July 2005

Stacked films of chromium oxide and chromium (Cr2O3/Cr) have been commonly used as a photomask for the lithographic process of integrated circuit fabrication. It has been found, however, that the Cr2O3/Cr films were etched during the oxygen plasma ashing process, which is applied for the resist removal after the Cr2O3/Cr patterning. In order to solve this problem, we investigated the mechanisms of the Cr2O3/Cr film etching during the ashing process. As a result, it was found that the Cr2O3/Cr film is oxidized during the ashing process to generate CrO
x
(2≤x≤3) in which Cr has a higher valence than Cr2O3, and that the CrO
x
(2≤x≤3) evaporates. It was confirmed by means of a plasma shielding experiment that not only oxygen plasma but also oxygen radicals oxidize the Cr2O3/Cr. It has been found that keeping the photomask temperature below 200°C during the ashing process solves the Cr2O3/Cr etching problem.
Activation Behavior of Boron and Phosphorus Atoms Implanted in Polycrystalline Silicon Films by Heat Treatment at 250°C
Authors: Sameshima Toshiyuki , Andoh Nobuyuki , Andoh Yasunori
Published: July 2005

The activation behavior of boron and phosphorus implanted into laser-crystallized silicon films were investigated. The ratio of recrystallization of an ion-doping-induced amorphous region by heat treatment at 250°C was 0.35 for a boron concentration lower than 6.4×1019 cm-3 and 0.5 for a phosphorus concentration lower than 2.5×1019 cm-3. This ratio decreased as dopant concentration increased. High electrical conductivities of 1.1×102 S/cm and 7.3 S/cm were achieved by oxygen plasma treatment at 250°C for 1 h in the cases of 3.2×1020-cm-3 boron and 5.0×1019-cm-3-phosphorus doping, respectively. Numerical analysis of the electrical conductivity revealed that the electrical conductivity was governed by recrystallization ratio and the density of the intrinsic defects of polycrystalline films.
Temperature Dependences of Electric Resistivity and Thermoelectric Power on Sn Fraction X in Polycrystalline n-AgIn1-XSnXO2 Compounds
Authors: Kajiwara Toshiro , Yoshiara Kiichi
Published: July 2005

Polycrystalline n-AgIn1-X
Sn
X
O2 (X=0.03, 0.05, 0.07 and 0.10) with the delafossite structure were prepared, and the temperature dependences of their thermoelectric properties were evaluated to determine power factor. The most suitable power factor was obtained at X=0.05. The electric resistivity and thermoelectric power of the polycrystalline n-AgIn0.95Sn0.05O2 specimen were 5×10-4 Ωm and -150 µV K-1 at 500°C, respectively. These results indicate the possibility of applying these crystals in supplemental electric power generators of automobiles.
Non-d-wave Behavior Observed in Low-Temperature Specific Heat of Pr1.85Ce0.15CuO4.065
Authors: Meen Teen-Hang , Huang Chien-Jung , Shu Mou-Shin , Li Jiun-Wei , Li Tsz-Tai , Chen Wen-Ray
Published: July 2005

Recently, possible evidence from the low-temperature specific heat (LTSH) for the lines of nodes in the superconducting order parameter of cuprate superconductors has attracted considerable attention and is still a controversial issue. To clarify this issue, N-type Pr1.85Ce0.15CuO4+δ samples have been prepared under different annealing conditions and investigated by means of X-ray diffraction and oxygen content analyses, and magnetic-susceptibility and low-temperature specific heat (LTSH) measurements. The values of oxygen content parameter δ for Pr1.85Ce0.15CuO4+δ are 0.161 and 0.065 for samples annealed in an Ar atmosphere and in vacuum, respectively. Pr1.85Ce0.15CuO4.161 shows clear evidence for an αT
2 term at zero magnetic field in LTSH measurements, which is consistent with d-wave superconductivity. However, this behavior is not observed in Pr1.85Ce0.15CuO4.065. These results indicate that different heat treatments may change the oxygen content of Pr1.85Ce0.15CuO4+δ, resulting in the different behaviors observed in LTSH measurements. We also discuss the results of the LTSH measurements in La2-x
Sr
x
CuO4 (x=0.1, 0.16 and 0.22) to explain these behaviors observed in the LTSH data of Pr1.85Ce0.15CuO4+δ.
Effect of Light Illumination on Magnetization in Metamagnet Fe3Ga4 Grains Formed on GaAs Substrates
Authors: Jamil Abu Talib MD Kaosar , Noguchi Hiroshi , Shiratori Koya , Kondo Tsuyoshi , Munekata Hiro
Published: July 2005

Light-induced enhancement in magnetization is observed at room temperature in the metamagnetic Fe3Ga4 grains formed by the alternative deposition of Fe3Ga2-x
As
x
and GaAs on GaAs(001) substrates. The illumination power dependence of the enhanced magnetization is compared with the antiferromagnetic-type magnetization–temperature (M–T) curve (Néel temperature of T
N=340–390 K), and, in addition with the enhancement due to light-induced heating, the possibility of photoenhanced magnetization is discussed.
Preparation and Magnetic Properties of Ni0.36Zn0.64 Ferrite from Microwave-Induced Combustion
Authors: Fu Yen-Pei , Hsu Chin-Shang , Tay Kok-Wan
Published: July 2005

Ni–Zn ferrite powders were successfully synthesized using microwave induced combustion. The process took only 15 min to obtain as-received Ni–Zn ferrite powders. The resultant powders were annealed at different temperatures and were investigated by differential thermal analysis/thermogravimetry (TG/DTA), X-ray diffractometry (XRD), transmission electron microscopy (TEM), scanning electron microscopy (SEM), and vibrating sample magnetometry (VSM). The as-received powders showed the formation of cubic ferrite with saturation magnetization (M
s) of 23 emu/g and an intrinsic coercive force (H
c) of 135 Oe, whereas upon annealing at 850°C for 2 h, the saturation magnetization increases to 58 emu/g and the intrinsic coercive force reached 197 Oe. The toroidal specimen sintered at 1200°C for 2 h presented both an optimum initial permeability (µi) and quality factor (Q). The high initial permeability and large quality factor were closely associated with effective improvement of the densification and magnetic characteristics properties of sintered specimen made from nanosized Ni–Zn ferrite powder prepared by microwave-induced combustion.
Dependence of Electrode on Switching Effect of Pr1-xCaxMnO3 Thin Film
Authors: Kim Chang Jung , Kim Byung Ik , Chen I-Wei
Published: July 2005

We examined the effect of top-electrode materials on the electric-pulse-induced resistance (EPIR) change property of Pr1-x
Ca
x
MnO3 (PCMO) thin films grown on a Pt/Ti/SiO2/Si substrate. To investigate the top-electrode effect, we used Al, Pt, Au/Cr and Au (10%)–Pd (90%) alloy metals as the top electrodes on PCMO films with a Pt bottom electrode. The thin films with an Al top and a Au/Cr electrode exhibited EPIR switching phenomena. With a top electrode of 75 µm diameter circle, the Pr0.7Ca0.3MnO3 film shows a low resistance in the range of 20–40 Ω. The ratio between low resistance and high resistance is approximately 2 under an applied single pulse of 50 ns duration and ±4 V magnitude. On the contrary, the thin films with Pt and Au–Pd alloy top electrodes exhibited no EPIR switching.