bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measurement of wafer temperature variations using photoresist reticulation thresholds
Authors: Luckman Gregory 
Published: July 2002

This article presents a technique for using the onset of reticulation, or hazing, of a novolac-diazonaphthoquinone (DNQ) photoresist to monitor differences in peak temperatures between silicon wafers subjected to plasma processing. The technique exploits the lowering of the reticulation threshold temperature with progressive light exposure and consequent photolysis of the resist’s DNQ photoactive compound. Either near ultraviolet or white fluorescent room lights can serve as the light exposure source and are used to establish areas on a wafer with varying concentrations of DNQ. With a range of reticulation threshold temperatures present on a single wafer, wider plasma process latitude is achieved. This makes it more likely that reticulation occurs at least somewhere on a wafer. It also makes it easy to compare results on different wafers by comparing the areas that reticulate. The method resembles the use of thermal dots, but employs only the resist materials commonly present in plasma etching processes. The technique is simple, cheap, and requires no viewports or feedthroughs. Using the technique, it is shown that wafers become hotter on a bare aluminum electrode than on an anodized aluminum electrode and that silicon wafers partially transparent in the infrared become hotter than those opaque in the infrared. The results also demonstrate the degree of temperature uniformity between wafers in a batch tool. Further applications of the technique are suggested. Literature on resist degradation in plasma is reviewed and a new microscopic mechanism is proposed for the reticulation that causes the hazy resist film appearance.
The mechanism is a phase separation of unmodified resist polymer chain molecules from polymer chain molecules modified by exposure to the plasma. The proposed mechanism is used as an heuristic model for assessing the accuracy of a calibration procedure for the hazing onset temperature, which is also presented. The calibration exploits the fact that hazing of a resist film on a wafer occurs if the wafer is subjected to a plasma process and then ramped up in temperature on a hot plate. The calibration procedure exploits the variation of reticulation temperature with DNQ conversion. Under one set of run conditions the calibration indicated a peak wafer temperature between 406 and 412 K. This was compared to a calibration using thermal dots, which indicated a peak temperature between 400 and 405 K, and with the stated thermal flow temperature of the resist, 398 K. The calibration results indicate the limitations of relying on resist thermal flow data to estimate peak wafer temperatures in plasma processes.
Frequent Association between Alteration of the
rdxA
Gene and Metronidazole Resistance in French and North African Isolates of
Helicobacter pylori
Authors: Tankovic Jacques , Lamarque Dominique , Delchier Jean-Charles , Soussy Claude-James , Labigne Agnes , Jenks Peter J. 
Published: July 2002

ABSTRACT

Mutations in the
rdxA
gene have been associated with the acquisition of resistance to metronidazole in
Helicobacter pylori
. This gene encodes an NADPH nitroreductase whose expression is necessary for intracellular activation of the drug. We wished to examine whether mutations in
rdxA
were present in resistant
H. pylori
isolates infecting either French or North African patients. We determined the complete nucleotide sequences of the
rdxA
genes from seven French and six North African patients infected with paired resistant and sensitive strains. Genotyping by random amplified polymorphic DNA analysis confirmed the close genetic relatedness of the susceptible and resistant isolates from individual biopsies. Eight French and five North African individual resistant strains were also studied. For the French strains, an alteration in
rdxA
most probably implicated in resistance was found in 10 cases (seven frameshift mutations, two missense mutations, and one deletion of 211 bp). One to three putative missense mutations were identified in four cases, and a missense mutation possibly not implicated in resistance was discovered in the last case. For the North African strains, an alteration in
rdxA
was found in eight cases (three frameshift mutations, three missense mutations, one deletion of 6 bp, and one insertion of a variant of IS
605
). Two strains contained putative missense mutations, and no change was observed in
rdxA
of the last strain. Thus, inactivation of the
rdxA
gene is frequently, but not always, associated with resistance to metronidazole in French and North African clinical isolates of
H. pylori
. In addition, a variety of alterations of
rdxA
are associated with the resistant phenotype.
Molecular and Biochemical Analysis of AST-1, a Class A β-Lactamase from
Nocardia asteroides
Sensu Stricto
Authors: Poirel Laurent , Laurent Frederic , Naas Thierry , Labia Roger , Boiron Patrick , Nordmann Patrice 
Published: July 2002

ABSTRACT

A β-lactamase gene was cloned from a
Nocardia asteroides
sensu stricto clinical isolate. A recombinant plasmid, pAST-1, expressed the β-lactamase AST-1 in
Escherichia coli
JM109. Its pI was 4.8, and its relative molecular mass was 31 kDa.
E. coli
JM109(pAST-1) was resistant to penicillins and narrow-spectrum cephalosporins. The β-lactamase AST-1 had a restricted hydrolytic activity spectrum. Its activity was partially inhibited by clavulanic acid but not by sulbactam and tazobactam. AST-1 is an Ambler class A β-lactamase sharing 65% amino acid identity with β-lactamase FAR-1, the most closely related enzyme.
Starvation Improves Survival of Bacteria Introduced into Activated Sludge
Authors: Watanabe Kazuya , Miyashita Mariko , Harayama Shigeaki 
Published: July 2002

ABSTRACT

A phenol-degrading bacterium,
Ralstonia eutropha
E2, was grown in Luria-Bertani (LB) medium or in an inorganic medium (called MP) supplemented with phenol and harvested at the late-exponential-growth phase. Phenol-acclimated activated sludge was inoculated with the E2 cells immediately after harvest or after starvation in MP for 2 or 7 days. The densities of the E2 populations in the activated sludge were then monitored by quantitative PCR. The E2 cells grown on phenol and starved for 2 days (P-2 cells) survived in the activated sludge better than those treated differently: the population density of the P-2 cells 7 days after their inoculation was 50 to 100 times higher than the population density of E2 cells without starvation or that with 7-day starvation. LB medium-grown cells either starved or nonstarved were rapidly eliminated from the sludge. The P-2 cells showed a high cell surface hydrophobicity and retained metabolic activities. Cells otherwise prepared did not have one of these two features. From these observations, it is assumed that hydrophobic cell surface and metabolic activities higher than certain levels were required for the inoculated bacteria to survive in the activated sludge. Reverse transcriptase PCR analyses showed that the P-2 cells initiated the expression of phenol hydroxylase within 1 day of their inoculation into the sludge. These results suggest the utility of a short starvation treatment for improving the efficacy of bioaugumentation.
Molecular and Immunological Analyses of the
Borrelia turicatae
Bdr Protein Family
Authors: Carlyon Jason A. , Roberts David M. , Theisen Michael , Sadler Christina , Marconi Richard T. 
Published: July 2002

ABSTRACT

Here, we describe the molecular and immunological characterization of the
bdr
gene family of
Borrelia turicatae
, a relapsing-fever spirochete. Nine
bdr
alleles belonging to two different subfamilies were sequenced and localized to linear plasmids. Anti-Bdr antiserum was generated and used to analyze Bdr expression in pre- and postinfection isogenic populations. The analyses presented here provide a detailed characterization of the Bdr proteins in a relapsing-fever spirochete species, enhancing our understanding of these proteins at the genus-wide level.
Lyme Arthritis Resolution with Antiserum to a 37-KilodaltonBorrelia burgdorferiProtein
Authors: Feng Sunlian , Hodzic Emir , Barthold Stephen W. 
Published: July 2002

ABSTRACTA 37-kDa protein fromBorrelia burgdorferi(the agent of Lyme disease) was identified as a target for immune-mediated resolution of Lyme arthritis. Studies in a mouse model have shown that arthritis resolution can be mediated by antibodies (against unknown target antigens) within immune sera from actively infected mice. Immune sera from infected mice were therefore used to screen aB. burgdorferigenomic expression library. A gene was identified whose native product is a putative lipoprotein of approximately 37 kDa, referred to here as arthritis-related protein (Arp). Active and passive immunization of mice with recombinant Arp or Arp antiserum, respectively, did not protect mice from challenge inoculation. However, when Arp antiserum was administered to severe combined immunodeficient (SCID) mice with established infections and with ongoing arthritis and carditis, treatment selectively induced arthritis resolution without affecting the status of carditis or influencing the status of infection, including spirochetemia. The selective arthritis-resolving effect of Arp antiserum mimics the activity of immune serum from immunocompetent mice when such serum is transferred into SCID mice with established infections. Thearpgene could not be amplified from unrelatedB. burgdorferiisolates but hybridized with those isolates only under very-low-stringency conditions. Arp antiserum reacted against proteins of similar size in a wide range ofB. burgdorferiisolates.
Helicobacter pylori
Pore-Forming Cytolysin Orthologue TlyA Possesses In Vitro Hemolytic Activity and Has a Role in Colonization of the Gastric Mucosa
Authors: Martino M. Celeste , Stabler Richard A. , Zhang Zun W. , Farthing Michael J. G. , Wren Brendan W. , Dorrell Nick 
Published: July 2002

ABSTRACT

Hemolysins have been found to possess a variety of functions in bacteria, including a role in virulence.
Helicobacter pylori
demonstrates hemolytic activity when cultured on unlysed blood agar plates which is increased under iron-limiting conditions. However, the role of an
H. pylori
hemolysin in virulence is unclear. Scrutiny of the
H. pylori
26695 genome sequence suggests the presence of at least two distinct hemolysins, HP1086 and HP1490, in this strain. Previous studies have shown that the in vitro hemolytic activity of
H. pylori
is reduced when it is coincubated with dextran 5000, suggesting the presence of a pore-forming cytolysin. HP1086 has homology to pore-forming cytolysins (TlyA) from other bacterial species, and the introduction of the cloned
H. pylori tlyA
gene into a nonhemolytic
Escherichia coli
strain conferred hemolytic activity. An
H. pylori tlyA
defined mutant showed reduced in vitro hemolytic activity, which appears to be due to pore formation, as the hemolytic activity of the wild-type strain is reduced to the same level as the
tlyA
mutant by the addition of dextran 5000. The mutant also showed reduced adhesion to human gastric adenocarcinoma cells and failed to colonize the gastric mucosa of mice. These data clearly suggest a role in virulence for
H. pylori
TlyA, contrary to the suggestion that hemolytic activity is an in vitro phenomenon for this pathogen.
Site-Specific Mutational Analysis of a Novel Cysteine Motif Proposed To Ligate the 4Fe-4S Cluster in the Iron-Sulfur Flavoprotein of the Thermophilic Methanoarchaeon
Methanosarcina thermophila
Authors: Leartsakulpanich Ubolsree , Antonkine Mikhail L. , Ferry James G. 
Published: July 2002

ABSTRACT

Isf (iron-sulfur flavoprotein) from
Methanosarcina thermophila
has been produced in
Escherichia coli
as a dimer containing two 4Fe-4S clusters and two FMN (flavin mononucleotide) cofactors. The deduced sequence of Isf contains six cysteines (Cys 16, Cys 47, Cys 50, Cys 53, Cys 59, and Cys 180), four of which (Cys 47, Cys 50, Cys 53, and Cys 59) comprise a motif with high identity to a motif (CX
2
CX
2
CX
4–7
C) present in all homologous Isf sequences available in the databases. The spacing of the motif is highly compact and atypical of motifs coordinating known 4Fe-4S clusters; therefore, all six cysteines in Isf from
M. thermophila
were altered to either alanine or serine to obtain corroborating biochemical evidence that the motif coordinates the 4Fe-4S cluster and to further characterize properties of the cluster dependent on ligation. All except the C16S variant were produced in inclusion bodies and were void of iron-sulfur clusters and FMN. Reconstitution of the iron-sulfur cluster and FMN was attempted for each variant. The UV-visible spectra of all reconstituted variants indicated the presence of iron-sulfur clusters and FMN. The reduced C16A/S variants showed the same electron paramagnetic resonance (EPR) spectra as wild-type Isf, whereas the reduced C180A/S variants showed EPR spectra identical to those of one of the two 4Fe-4S species present in the wild-type Isf spectrum. Conversely, EPR spectra of the oxidized C50A and C59A variants showed
g
values characteristic of a 3Fe-4S cluster. The spectra of the C47A and C53A variants indicated a 4Fe-4S cluster with
g
values and linewidths different from those for the wild type. The combined results of this study support a role for the novel CX
2
CX
2
CX
4–7
C motif in ligating the 4Fe-4S clusters in Isf and Isf homologues.
Function-Based Selection and Characterization of Base-Pair Polymorphisms in a Promoter of
Escherichia coli
RNA Polymerase-ς
70
Authors: Xu Jian , McCabe Barbara C. , Koudelka Gerald B. 
Published: July 2002

ABSTRACT

We performed two sets of in vitro selections to dissect the role of the −10 base sequence in determining the rate and efficiency with which
Escherichia coli
RNA polymerase-ς
70
forms stable complexes with a promoter. We identified sequences that (i) rapidly form heparin-resistant complexes with RNA polymerase or (ii) form heparin-resistant complexes at very low RNA polymerase concentrations. The sequences selected under the two conditions differ from each other and from the consensus −10 sequence. The selected promoters have the expected enhanced binding and kinetic properties and are functionally better than the consensus promoter sequence in directing RNA synthesis in vitro. Detailed analysis of the selected promoter functions shows that each step in this multistep pathway may have different sequence requirements, meaning that the sequence of a strong promoter does not contain the optimal sequence for each step but instead is a compromise sequence that allows all steps to proceed with minimal constraint.
Characterization of an rRNA Operon (
rrnB
) of
Mycobacterium fortuitum
and Other Mycobacterial Species: Implications for the Classification of Mycobacteria
Authors: Menendez M. C. , Garcia M. J. , Navarro M. C. , Gonzalez-y-Merchand J. A. , Rivera-Gutierrez S. , Garcia-Sanchez L. , Cox R. A. 
Published: July 2002

ABSTRACT

Mycobacteria are thought to have either one or two rRNA operons per genome. All mycobacteria investigated to date have an operon, designated
rrnA
, located downstream from the
murA
gene. We report that
Mycobacteriun fortuitum
has a second
rrn
operon, designated
rrnB
, which is located downstream from the
tyrS
gene;
tyrS
is very close to the 3" end of a gene (
3-mag
) coding for 3-methylpurine-DNA-glycosylase. The second
rrn
operon of
Mycobacterium smegmatis
was shown to have a similar organization, namely, 5"
3-mag
-
tyrS
-
rrnB
3". The
rrnB
operon of
M. fortuitum
was found to have a single dedicated promoter. During exponential growth in a rich medium, the
rrnB
and
rrnA
operons were the major and minor contributors, respectively, to pre-rRNA synthesis. Genomic DNA was isolated from eight other fast-growing mycobacterial species. Samples were investigated by Southern blot analysis using probes for
mur
A,
tyrS
, and 16S rRNA sequences. The results revealed that both
rrnA
and
rrnB
operons were present in each species. The results form the basis for a proposed new scheme for the classification of mycobacteria. The approach, which is phylogenetic in concept, is based on particular properties of the
rrn
operons of a cell, namely, the number per genome and a feature of 16S rRNA gene sequences.
The Simian Virus 40 Core Origin Contains Two Separate Sequence Modules That Support T-Antigen Double-Hexamer Assembly
Authors: Sreekumar K. R. , Prack Andrea E. , Winters Danielle R. , Barbaro Brett A. , Bullock Peter A. 
Published: July 2002

ABSTRACT
Using subfragments of the simian virus 40 (SV40) core origin, we demonstrate that two alternative modules exist for the assembly of T-antigen (T-ag) double hexamers. Pentanucleotides 1 and 3 and the early palindrome (EP) constitute one assembly unit, while pentanucleotides 2 and 4 and the AT-rich region constitute a second, relatively weak, assembly unit. Related studies indicate that on the unit made up of pentanucleotide 1 and 3 and the EP assembly unit, the first hexamer forms on pentanucleotide 1 and that owing to additional protein-DNA and protein-protein interactions, the second hexamer is able to form on pentanucleotide 3. Oligomerization on the unit made up of pentanucleotide 2 and 4 and the AT-rich region is initiated by assembly of a hexamer on pentanucleotide 4; subsequent formation of the second hexamer takes place on pentanucleotide 2. Given that oligomerization on the SV40 origin is limited to double-hexamer formation, it is likely that only a single module is used for the initial assembly of T-ag double hexamers. Finally, we discuss the evidence that nucleotide hydrolysis is required for the remodeling events that result in the utilization of the second assembly unit.
Human Immunodeficiency Virus Type 1 Nef Mediates Sustained Membrane Expression of Tumor Necrosis Factor and the Related Cytokine LIGHT on Activated T Cells
Authors: Lama Juan , Ware Carl F. 
Published: July 2002

ABSTRACTHuman immunodeficiency virus (HIV) Nef downregulates the antigen recognition molecules major histocompatibility complex class I and CD4. Downregulation of surface CD4 by Nef relies on the ability of this viral protein to redirect the endocytic machinery to CD4. However, by redirecting the endocytic machinery, Nef may affect the internalization rates of other proteins. Here we show that Nef simultaneously enhances surface expression of the effector cytokines tumor necrosis factor (TNF) and LIGHT, leading to enhanced cytokine activity. A dileucine motif in Nef, which is essential for CD4 downregulation and is involved in the recruitment of adapter protein complexes by Nef, was required to increase surface levels of both cytokines. The physiological impact of the Nef-mediated interference with endocytosis was demonstrated by the fact that a TNF-responsive T-cell line chronically infected with HIV produced higher levels of p24 viral protein following expression of a Nef-green fluorescent protein (GFP) fusion protein. This enhancement was dependent on the levels of membrane-bound TNF, since it was abrogated by a recombinant soluble TNF receptor. Expression of Nef-GFP in human 293T cells reduced the endocytosis of LIGHT, whereas at the same time CD4 internalization was accelerated. Taken together, these results suggest that in infected cells Nef interferes with the internalization of these effector cytokines. By increasing TNF expression, Nef could accelerate disease progression in infected individuals. These findings may help explain the pleiotropic functions that Nef plays during infection and disease.
The E1 Initiator Recognizes Multiple Overlapping Sites in the Papillomavirus Origin of DNA Replication
Authors: Chen Grace , Stenlund Arne 
Published: July 2002

ABSTRACT
A common feature of replicator sequences from a variety of organisms is multiple binding sites for an initiator protein. By binding to the replicator, initiators mark the site and contribute to melting or distortion of the DNA. We have defined the recognition sequence for the papillomavirus E1 initiator and determined the arrangement of binding sites in the viral origin of replication. We show that E1 recognizes a hexanucleotide sequence which is present in overlapping arrays in virtually all papillomavirus replicators. Binding of the initiator to these sites would result in the formation of a closely packed array of E1 molecules that wrap around the double helix.
In Vivo Selection of a Lymphocytic Choriomeningitis Virus Variant That Affects Recognition of the GP33-43 Epitope by H-2Dbbut Not H-2Kb
Authors: Puglielli Maryann T. , Zajac Allan J. , van der Most Robbert G. , Dzuris John L. , Sette Alessandro , Altman John D. , Ahmed Rafi 
Published: July 2002

ABSTRACTCD8 T cells drive the protective immune response to lymphocytic choriomeningitis virus (LCMV) infection and are thus a determining force in the selection of viral variants. To examine how escape mutations affect the presentation and recognition of overlapping T-cell epitopes, we isolated an LCMV variant that is not recognized by T-cell receptor (TCR)-transgenic H-2Db-restricted LCMV GP33-41-specific cytotoxic T lymphocytes (CTL). The variant virus carried a single-amino-acid substitution (valine to alanine) at position 35 of the viral glycoprotein. This region of the LCMV glycoprotein encodes both the Db-restricted GP33-43 epitope and a second epitope (GP34-42) presented by the Kbmolecule. We determined that the V-to-A CTL escape mutant failed to induce a DbGP33-43-specific CTL response and that Db-restricted GP33-43-specific CTL induced by the wild-type LCMV strain were unable to kill target cells infected with the variant LCMV strain. In contrast, the Kb-restricted response was much less affected. We found that the V-to-A substitution severely impaired peptide binding to Dbbut not to Kbmolecules. Strikingly, the V-to-A mutation did not change any of the anchor residues, and the dramatic effect on binding was therefore unexpected. The strong decrease in Dbbinding explains why the variant virus escapes the DbGP33-43-specific response but still elicits the Kb-restricted response. These findings also illustrate that mutations within regions encoding overlapping T-cell epitopes can differentially affect the presentation and recognition of individual epitopes.