bluuebunny/crossref_metadata_2025 huggingface dataset:
Characteristics of ultrathin SiO2 films using dry rapid thermal oxidation and Pt catalyzed wet oxidation
Authors: Cho M.-H. , Shin J. S. , Roh Y. S. , Lyo I.-W. , Jeong K. , Whang C. N. , Lee J. S. , Yoo J. Y. , Lee N. I. , Fujihara K. , Moon Dae Won
Published: July 2003

The SiO2/Si interfaces of the 2 nm thick dry oxide using rapid thermal oxidation and wet oxide using H2O formed by catalysis of Pt were investigated in order to understand the difference between the two oxides relevant to the device reliability using various methods. The interstitial defects at the interfacial region were detected using medium energy of ion scattering spectroscopy in the sample of dry oxidation, but not in the wet oxidation. The interfacial roughness and the interstitial defects strongly depended on the oxidation process, although the interfacial strain differs very little between the dry and wet oxidation processes. The results of high resolution x-ray photoelectron spectroscopy using a synchrotron radiation source clearly provided the difference of the defects between two oxides. The scanning tunneling microscope image of the SiO2 layers subjected to hot electron injection from the tip showed that wet oxide had superior quasi-breakdown characteristics to dry oxide. Time-dependent dielectric breakdown of the SiO2 layer also depended on the oxidation process, indicating that the interface roughness and the defects critically affect the reliability of the gate oxide. Thus the wet oxidized SiO2 film is found to be more stable against the dielectric breakdown than the dry oxidized sample.
Fabrication of microstructured copper on an indium–tin–oxide surface using a micropatterned self-assembled monolayer as a template
Authors: Asakura Shuuichi , Hirota Mitsuhito , Fuwa Akio
Published: July 2003

The difference in chemical reactivity between indium–tin–oxide (ITO) and self-assembled monolayer (SAM) surfaces was used to fabricate copper (Cu) microstructures. ITO substrates coated with octadecyltrimethoxysilane (ODS)–SAM were photolithographically micropatterned using vacuum ultraviolet (VUV) light. Each of the micropatterned samples was subsequently immersed in an electrodeposition bath in order to deposit Cu on its surface. As confirmed by atomic force microscopy, Cu electrodeposition proceeded selectively on the VUV-irradiated areas of the ITO surface while the ODS–SAM surface served effectively as a mask to block Cu deposition. Cu microstructures with 7.5 × 7.5 μm2 features were successfully fabricated on the ITO surface.
Growth and effects of remote-plasma oxidation on thin films of HfO2 prepared by metal-organic chemical-vapor deposition
Authors: Yamamoto Kazuhiko , Asai Masayuki , Horii Sadayoshi , Miya Hironobu , Niwa Masaaki
Published: July 2003

The metal-organic (MO) chemical vapor deposition of hafnium oxide (HfO2) films from a new MO precursor, Hf(OC(CH3)2CH2OCH3)4, was investigated. The deposition rate of HfO2 is higher when oxygen gas is being supplied with the precursor. However, films deposited in the presence of added oxygen contain large amounts of H2O due to oxidation of the Hf precursor. O2 addition process degraded HfO2 film properties. In situ remote-plasma oxidation (RPO) is found to be effective in reducing the contaminants in HfO2. Leakage current in HfO2/Si capacitors with TiN gate electrode is also shown to be lower when deposition is without the oxygen addition and RPO treatment is subsequently performed.
Effects of high working pressure on dielectric properties of sputtered (Ba,Sr)TiO3 films on Ir electrodes
Authors: Lai Chih-Haung , Wu Y. C. , Ma S.
Published: July 2003

High working pressure (47 mTorr) was used for rf-sputtered (Ba,Sr)TiO3 (BST) films on Ir bottom electrodes to enhance the in situ formation of IrO2 without postannealing. We verified that oxygen plasma bombardment on the Ir surface during the deposition of BST films was the dominant mechanism for in situ IrO2 formation under the condition of high working pressure. The as-deposited BST film of 100 nm grown at 500 °C shows a high dielectric constant of 630 (at 10 kHz); however, the leakage current is relatively large (6×10−5 A/cm2 at 100 kV/cm). The large leakage current results from the rough interface due to the formation of thick IrO2. To reduce leakage current, the double-layer technology was used, in which a thin BST film (5 nm) was first deposited with pure Ar, and followed by the deposition of a thick film (95 nm) with mixture gas (Ar/O2=1). The thin BST layer can significantly reduce the roughness of IrO2, resulting in lower leakage current (4×10−7 A/cm2); however, since the thin BST layer is oxygen deficient, the dielectric constant is reduced to 443.
Inorganic electret using SiO2 thin films prepared by radio-frequency magnetron sputtering
Authors: Minami Tadatsugu , Utsubo Tetsuharu , Miyata Toshihiro , Ohbayashi Yoshiaki
Published: July 2003

Inorganic thin-film electrets that exhibited high surface potential stability in a highly humid atmosphere were fabricated using SiO2 thin films prepared by radio-frequency magnetron sputtering and heat treated at highly humid atmosphere at a high temperature. The obtainable stability was considerably affected by not only the heat treatment conditions but also the deposition conditions of the SiO2 films. High surface potential stability and remaining potential were obtained for SiO2 thin films heat treated in a highly humid atmosphere at a temperature of 400 °C for 60 min. The deposition conditions were optimized: substrate temperature of about 360 °C, sputter gas pressure (Ar+O2) of 0.35 Pa with O2 partial pressure of 20%, and target of fused quartz. The surface potential of SiO2 thin films fabricated with a thickness of 2.5–10 μm under optimized deposition and heat-treatment conditions was found to exhibit no degradation when tested for longer than 50 h at a relative humidity of 90% and a temperature of 60 °C.
Quasi-nonpropagating wave sources in one dimension
Authors: Denardo Bruce , Miller Gregg L.
Published: July 2003

When a medium is driven by a spatially extended wave source, it is possible that no waves emanate from the driven region and a standing wave occurs inside the region. This case is a nonpropagating wave source. We report numerical observations and theory in one dimension, where the realistic effects of weak dissipation and weak nonuniformity are included. Each of the effects causes a small amount of propagation to occur so that the source becomes quasi-nonpropagating. The amplitude of the outgoing wave compared to the amplitude of the standing wave is substantially reduced for a uniform source compared to a two-point source of the same length, which suggests that the more evenly a source is spread over a fixed length, the less is the relative propagation.
Generalization of the electrostatic potential function for an infinite charge distribution
Authors: Palma G. , Oyarzún R. , Raff U.
Published: July 2003

The asymptotic conditions needed to define the electrostatic potential due to an infinite charge distribution are studied in detail. It is shown that if the charge distribution decreases faster than the square of the distance when |r| goes to infinity, the convolution integral defining the potential exists, goes to zero as |r| goes to infinity, and therefore allows the calculation of the electric potential function at any point in space, even if the total charge is infinite. We illustrate the calculation of the electric potential with a simple example of a spherically symmetric infinite charge distribution.
A novel empirical study of the photoelectric effect in thin gold films
Authors: Earle G. D. , Copp B. L. , Klenzing J. H. , Bishop R. L.
Published: July 2003

We describe a simple experiment designed to stimulate deeper understanding of the photoelectric effect, including the effects of thin metal films on both incident ultraviolet photons and liberated photoelectrons. Interpretation of the results teaches principles of critical thinking and curve-fitting that can benefit students throughout their scientific careers.
What happens to energy and momentum when two oppositely-moving wave pulses overlap?
Authors: Gauthier N.
Published: July 2003

The overlap of two wave pulses that are moving in opposite directions along the same line in a linear, nondissipative and nondispersive medium is used to discuss the compatibility of wave superposition and of energy–momentum conservation. What happens to the energy and to the momentum when the pulses overlap in such a situation is examined. The treatment is applicable to electromagnetic waves or to small-amplitude linear mechanical waves on an ideal string. It is argued that introductory-to-intermediate textbooks and the pedagogical literature have neglected these questions, particularly the one relating to the conservation of linear momentum.
Laser cooling and trapping visualized
Authors: Vredenbregt E. J. D. , van Leeuwen K. A. H.
Published: July 2003

Laser cooling and trapping have become widely used in the atomic physics laboratory. A computer program is presented that simulates some of the most important techniques employed, including atomic beam collimation, Zeeman slowing, funneling, and magneto-optical trapping. Its application ranges from experiment design to illustration of course material.
Crystal Structure of the GpIbα-Thrombin Complex Essential for Platelet Aggregation
Authors: Dumas John J. , Kumar Ravindra , Seehra Jasbir , Somers William S. , Mosyak Lidia
Published: July 2003

Direct interaction between platelet receptor glycoprotein Ibα (GpIbα) and thrombin is required for platelet aggregation and activation at sites of vascular injury. Abnormal GpIbα-thrombin binding is associated with many pathological conditions,including occlusive arterial thrombosis and bleeding disorders. The crystal structure of the GpIbα-thrombin complex at 2.6 angstrom resolution reveals simultaneous interactions of GpIbα with exosite I of one thrombin molecule,and with exosite II of a second thrombin molecule. In the crystal lattice,the periodic arrangement of GpIbα-thrombin complexes mirrors a scaffold that could serve as a driving force for tight platelet adhesion. The details of these interactions reconcile GpIbα-thrombin binding modes that are presently controversial,highlighting two distinct interfaces that are potential targets for development of novel antithrombotic drugs.
Modulation of α-Thrombin Function by Distinct Interactions with Platelet Glycoprotein Ibα
Authors: Celikel Reha , McClintock Richard A. , Roberts James R. , Mendolicchio G. Loredana , Ware Jerry , Varughese Kottayil I. , Ruggeri Zaverio M.
Published: July 2003

Thrombin bound to platelets contributes to stop bleeding and, in pathological conditions, may cause vascular thrombosis. We have determined the structure of platelet glycoprotein Ibα (GpIbα) bound to thrombin at 2.3 angstrom resolution and defined two sites in GpIbα that bind to exosite II and exosite I of two distinct α-thrombin molecules, respectively. GpIbα occupancy may be sequential, as the site binding to α-thrombin exosite I appears to be cryptic in the unoccupied receptor but exposed when a first thrombin molecule is bound through exosite II. These interactions may modulate α-thrombin function by mediating GpIbα clustering and cleavage of protease-activated receptors, which promote platelet activation, while limiting fibrinogen clotting through blockade of exosite I.
Tandem Transcription and Translation Regulatory Sensing of Uncharged Tryptophan tRNA
Authors: Chen Guangnan , Yanofsky Charles
Published: July 2003

The
Bacillus subtilis
AT (anti-TRAP) protein inhibits the regulatory protein TRAP (
trp
RNA-binding attenuation protein), thereby eliminating transcription termination in the leader region of the
trp
operon. Transcription of the AT operon is activated by uncharged tryptophan transfer RNA (tRNA
Trp
). Here we show that translation of AT also is regulated by uncharged tRNA
Trp
. A 10-residue coding region containing three consecutive tryptophan codons is located immediately preceding the AT structural gene. Completion of translation of this coding region inhibits AT synthesis, whereas incomplete translation increases AT production. Tandem sensing of uncharged tRNA
Trp
therefore regulates synthesis of AT, which in turn regulates TRAP's ability to inhibit
trp
operon expression.
Home of the Mind and More
Authors: Voogd Jan
Published: July 2003

Brain Architecture
Understanding the Basic Plan. Larry W. Swanson. Oxford University Press, New York, 2003. 281 pp. $59.50, £44.99 ISBN 0-19-510504-4. Paper, $29.95, £21.99. ISBN 0-19-510505-2.

Building on findings from theoretical and experimental morphology, embryology, and evolutionary biology, Swanson provides a balanced overview of the structure and function of the brain.
NhaR and RcsB Independently Regulate the
osmCp1
Promoter of
Escherichia coli
at Overlapping Regulatory Sites
Authors: Sturny Rachel , Cam Kaymeuang , Gutierrez Claude , Conter Annie
Published: July 2003

Transcription of the
Escherichia coli osmC
gene is induced by several stress conditions.
osmC
is expressed from two overlapping promoters,
osmCp1
and
osmCp2.
The proximal promoter,
osmCp2
, is transcribed at the entry into the stationary phase by the σ
s
sigma factor. The distal promoter,
osmCp1
, is activated by NhaR and RcsB. NhaR is a positive regulator of the LysR family and is known to be an activator of the
nhaA
gene encoding an Na
+
/H
+
antiporter. RcsB is the response regulator of the RcsCDB His-Asp phosphorelay signal transduction system. Genetic data indicated that activation of
osmCp1
by both NhaR and RcsB requires the same short sequences upstream of the −35 region of the promoter. Accordingly, DNase I footprint analysis indicated that both activators protect an overlapping region close to the −35 box of the promoter and suggested that the regulatory effect is direct. Despite the overlap of the binding sites, each activator acts independent of the other and is specific for a particular stress. NhaR can stimulate
osmCp1
in response to an osmotic signal even in the absence of RcsB. RcsB is responsible for the induction of
osmCp1
by alteration of the cell envelope, even in the absence of NhaR.
osmCp1
as an example of multiple-stress-responsive promoter is discussed in light of a comparison of the NhaR and RcsB target regions in the
Enterobacteriaceae
.
Interplay of the Czc System and Two P-Type ATPases in Conferring Metal Resistance to
Ralstonia metallidurans
Authors: Legatzki Antje , Grass Gregor , Anton Andreas , Rensing Christopher , Nies Dietrich H.
Published: July 2003

Cadmium and zinc are removed from cells of
Ralstonia metallidurans
by the CzcCBA efflux pump and by two soft-metal-transporting P-type ATPases, CadA and ZntA. The
czcCBA
genes are located on plasmid pMOL30, and the
cadA
and
zntA
genes are on the bacterial chromosome. Expression of
zntA
from
R
.
metallidurans
in
Escherichia coli
predominantly mediated resistance to zinc, and expression of
cadA
predominantly mediated resistance to cadmium. Both transporters decreased the cellular content of zinc or cadmium in this host. In the plasmid-free
R
.
metallidurans
strain AE104, single gene deletions of
cadA
or
zntA
had only a moderate effect on cadmium and zinc resistance, but zinc resistance decreased 6-fold and cadmium resistance decreased 350-fold in double deletion strains. Neither single nor double gene deletions affected zinc resistance in the presence of
czcCBA
. In contrast, cadmium resistance of the
cadA zntA
double mutant could be elevated only partially by the presence of CzcCBA.
lacZ
reporter gene fusions indicated that expression of
cadA
was induced by cadmium but not by zinc in
R
.
metallidurans
strain AE104. In the absence of the
zntA
gene, expression of
cadA
occurred at lower cadmium concentrations and zinc now served as an inducer. In contrast, expression of
zntA
was induced by both zinc and cadmium, and the induction pattern did not change in the presence or absence of CadA. However, expression of both genes,
zntA
and
cadA
, was diminished in the presence of CzcCBA. This indicated that CzcCBA efficiently decreased cytoplasmic cadmium and zinc concentrations. It is discussed whether these data favor a model in which the cations are removed either from the cytoplasm or the periplasm by CzcCBA.
immX
Immunity Region of
Rhizobium
Phage
16
-
3
: Two Overlapping Cistrons of Repressor Function
Authors: Csiszovszki Zsolt , Buzás Zsuzsanna , Semsey Szabolcs , Ponyi Tamás , Papp Péter P. , Orosz László
Published: July 2003

16
-
3
is a temperate phage of the symbiotic nitrogen-fixing bacterium
Rhizobium meliloti
41. Its prophage state and immunity against superinfection by homoimmune phages are governed by a complex set of controls: the
immC
and
immX
repressor systems and the
avirT
element are all located in well-separated, distinct regions which span 25 kb on the bacteriophage chromosome. The anatomy and function of the
immC
region are well documented; however, fewer analyses have addressed the
immX
and
avirT
regions. We focused in this paper on the
immX
region and dissected it into two major parts:
X

U/L

and
X

V

. The
X

U/L

part (0.6 kb) contained two overlapping cistrons,
X

U

and
X

L

, coding for proteins pXU and pXL, respectively. Inactivation of either gene inactivated the repressor function of the
immX
region. Loss-of-function mutants of
X

U

and
X

L

complemented each other in
trans
in double lysogens. The
X

V

part (1 kb) contained a target for
X

U/L

repressor action. Mutations at three sites in
X

V

led to various degree of ImmX insensitivity in a hierarchic manner. Two sites (
X

V1

and
X

V3

) exhibited the inverted-repeat structures characteristic of many repressor binding sites. However,
X

V1

could also be folded into a transcription terminator. Of the two immunity regions of
16
-
3
,
immX
seems to be unique both in its complex genetic anatomy and in its sequence. To date, no DNA or peptide sequence homologous to that of ImmX has been found in the data banks. In contrast,
immC
shares properties of a number of immunity systems commonly found in temperate phages.
Molecular Analysis of the
Enterococcus faecalis
Serotype 2 Polysaccharide Determinant
Authors: Hancock Lynn E. , Shepard Brett D. , Gilmore Michael S.
Published: July 2003

We previously described a 15-kb genetic cluster consisting of 11 open reading frames (
cps2A
to
cps2K
) of
Enterococcus faecalis
FA2-2 that is responsible for the production of the serotype 2 capsular polysaccharide. By using transcriptional fusions to a promoterless
lac
Z gene, we identified two independent promoters related to the expression of the polysaccharide. Both transcription initiation sites were mapped by primer extension. Reverse transcription-PCR (RT-PCR) demonstrated the transcriptional linkage of genes present in both transcripts. Real-time RT-PCR quantification of transcripts revealed maximum transcription during log phase growth, an observation confirmed by promoter fusion studies. The heterologous expression of this pathway in
Escherichia coli
caused reactivity with
E. faecalis
type 2 antiserum, thus demonstrating the essential role of this pathway in the synthesis of the type-specific polysaccharide.
The Glycosyltransferase Domain of Penicillin-Binding Protein 2a from
Streptococcus pneumoniae
Catalyzes the Polymerization of Murein Glycan Chains
Authors: Di Guilmi Anne Marie , Dessen Andréa , Dideberg Otto , Vernet Thierry
Published: July 2003

The bacterial peptidoglycan consists of glycan chains of repeating β-1,4-linked
N
-acetylglucosaminyl-
N
-acetylmuramyl units cross-linked through short peptide chains. The polymerization of the glycans, or glycosyltransfer (GT), and transpeptidation (TP) are catalyzed by bifunctional penicillin-binding proteins (PBPs). The β-lactam antibiotics inhibit the TP reaction, but their widespread use led to the development of drug resistance in pathogenic bacteria. In this context, the GT catalytic domain represents a potential target in the antibacterial fight. In this work, the in vitro polymerization of glycan chains by the extracellular region of recombinant
Streptococcus pneumoniae
PBP2a, namely, PBP2a* (the asterisk indicates the soluble form of the protein) is presented. Dansylated lipid II was used as the substrate, and the kinetic parameters
K

m

and
k
cat
/
K

m

were measured at 40.6 μM (± 15.5) and 1 × 10
−3
M
−1
s
−1
, respectively. The GT reaction catalyzed by PBP2a* was inhibited by moenomycin and vancomycin. Furthermore, the sequence between Lys 78 and Ser 156 is required for enzymatic activity, whereas it is dispensable for lipid II binding. In addition, we confirmed that this region of the protein is also involved in membrane interaction, independently of the transmembrane anchor. The characterization of the catalytically active GT domain of
S
.
pneumoniae
PBP2a may contribute to the development of new inhibitors, which are urgently needed to renew the antibiotic arsenal.
CsrA Regulates Translation of the
Escherichia coli
Carbon Starvation Gene,
cstA
, by Blocking Ribosome Access to the
cstA
Transcript
Authors: Dubey Ashok K. , Baker Carol S. , Suzuki Kazushi , Jones A. Daniel , Pandit Pallavi , Romeo Tony , Babitzke Paul
Published: July 2003

CsrA is a global regulator that binds to two sites in the
glgCAP
leader transcript, thereby blocking ribosome access to the
glgC
Shine-Dalgarno sequence. The upstream CsrA binding site (GCACACGGAU) was used to search the
Escherichia coli
genomic sequence for other genes that might be regulated by CsrA.
cstA
contained an exact match that overlapped its Shine-Dalgarno sequence.
cstA
was previously shown to be induced by carbon starvation and to encode a peptide transporter. Expression of a
cstA
′-′
lacZ
translational fusion in wild-type and
csrA
mutant strains was examined. Expression levels in the
csrA
mutant were approximately twofold higher when cells were grown in Luria broth (LB) and 5- to 10-fold higher when LB was supplemented with glucose. It was previously shown that
cstA
is regulated by the cyclic AMP (cAMP)-cAMP receptor protein complex and transcribed by Εσ
70
. We investigated the influence of σ
S
on
cstA
expression and found that a σ
S
deficiency resulted in a threefold increase in
cstA
expression in wild-type and
csrA
mutant strains; however, CsrA-dependent regulation was retained. The mechanism of CsrA-mediated
cstA
regulation was also examined in vitro. Cross-linking studies demonstrated that CsrA is a homodimer. Gel mobility shift results showed that CsrA binds specifically to
cstA
RNA, while coupled-transcription-translation and toeprint studies demonstrated that CsrA regulates CstA synthesis by inhibiting ribosome binding to
cstA
transcripts. RNA footprint and boundary analyses revealed three or four CsrA binding sites, one of which overlaps the
cstA
Shine-Dalgarno sequence, as predicted. These results establish that CsrA regulates translation of
cstA
by sterically interfering with ribosome binding.
Transcription and Analysis of Polymorphism in a Cluster of Genes Encoding Surface-Associated Proteins ofClostridium difficile
Authors: Savariau-Lacomme Marie-Pierre , Lebarbier Carole , Karjalainen Tuomo , Collignon Anne , Janoir Claire
Published: July 2003

Recent investigations of theClostridium difficilegenome have revealed the presence of a cluster of 17 genes, 11 of which encode proteins with similar two-domain structures, likely to be surface-anchored proteins. Two of these genes have been proven to encode proteins involved in cell adherence:slpAencodes the precursor of the two proteins of the S-layer, P36 and P47, whereascwp66encodes the Cwp66 adhesin. To gain further insight into the function of this cluster, we further focused onslpA,cwp66, andcwp84,the latter of which encodes a putative surface-associated protein with homology to numerous cysteine proteases. It displayed nonspecific proteolytic activity when expressed as a recombinant protein inEscherichia coli. Polymorphism ofcwp66andcwp84genes was analyzed in 28 strains, and transcriptional organization of the three genes was explored by Northern blots. TheslpAgene is strongly transcribed during the entire growth phase as a bicistronic transcript;cwp66is transcribed only in the early exponential growth phase as a polycistronic transcript encompassing the two contiguous genes upstream. The putative proteins encoded by the cotranscribed genes have no significant homology with known proteins but may have a role in adherence. No correlation could be established between sequence patterns of Cwp66 and Cwp84 and virulence of the strains. Thecwp84gene is strongly transcribed as a monocistronic message. This feature, together with the highly conserved sequence pattern ofcwp84, suggests a significant role in the physiopathology ofC. difficilefor the Cwp84 protease, potentially in the maturation of surface-associated adhesins encoded by the gene cluster.
IS
981
-Mediated Adaptive Evolution Recovers Lactate Production by
ldhB
Transcription Activation in a Lactate Dehydrogenase-Deficient Strain of
Lactococcus lactis
Authors: Bongers Roger S. , Hoefnagel Marcel H. N. , Starrenburg Marjo J. C. , Siemerink Marco A. J. , Arends John G. A. , Hugenholtz Jeroen , Kleerebezem Michiel
Published: July 2003

Lactococcus lactis
NZ9010 in which the
las
operon-encoded
ldh
gene was replaced with an erythromycin resistance gene cassette displayed a stable phenotype when grown under aerobic conditions, and its main end products of fermentation under these conditions were acetate and acetoin. However, under anaerobic conditions, the growth of these cells was strongly retarded while the main end products of fermentation were acetate and ethanol. Upon prolonged subculturing of this strain under anaerobic conditions, both the growth rate and the ability to produce lactate were recovered after a variable number of generations. This recovery was shown to be due to the transcriptional activation of a silent
ldhB
gene coding for an Ldh protein (LdhB) with kinetic parameters different from those of the native
las
operon-encoded Ldh protein. Nevertheless, cells producing LdhB produced mainly lactate as the end product of fermentation. The mechanism underlying the
ldhB
gene activation was primarily studied in a single-colony isolate of the recovered culture, designated
L
.
lactis
NZ9015. Integration of IS
981
in the upstream region of
ldhB
was responsible for transcription activation of the
ldhB
gene by generating an IS
981
-derived −35 promoter region at the correct spacing with a natively present −10 region. Subsequently, analysis of 10 independently isolated lactate-producing derivatives of
L
.
lactis
NZ9010 confirmed that the
ldhB
gene is transcribed in all of them. Moreover, characterization of the upstream region of the
ldhB
gene in these derivatives indicated that site-specific and directional IS
981
insertion represents the predominant mechanism of the observed recovery of the ability to produce lactate.
The Phosphate Starvation Stimulon ofCorynebacterium glutamicumDetermined by DNA Microarray Analyses
Authors: Ishige Takeru , Krause Malgorzata , Bott Michael , Wendisch Volker F. , Sahm Hermann
Published: July 2003

The phosphate (Pi) starvation stimulon ofCorynebacterium glutamicumwas characterized by global gene expression analysis by using DNA microarrays. Hierarchical cluster analysis of the genes showing altered expression 10 to 180 min after a shift from Pi-sufficient to Pi-limiting conditions led to identification of five groups comprising 92 genes. Four of these groups included genes which are not directly involved in P metabolism and changed expression presumably due to the reduced growth rate observed after the shift or to the exchange of medium. One group, however, comprised 25 genes, most of which are obviously related to phosphorus (P) uptake and metabolism and exhibited 4- to >30-fold-greater expression after the shift to Pilimitation. Among these genes, the RNA levels of thepstSCAB(ABC-type Piuptake system),glpQ(glycerophosphoryldiester phosphodiesterase),ugpAEBC(ABC-typesn-glycerol 3-phosphate uptake system),phoH(unknown function),nucH(extracellular nuclease), and Cgl0328 (5′-nucleotidase or related esterase) genes were increased, andpstSCABexhibited a faster response than the other genes. Transcriptional fusion analyses revealed that elevated expression ofpstSCABandugpAEBCwas primarily due to transcriptional regulation. Several genes also involved in P uptake and metabolism were not affected by Pistarvation; these included the genes encoding a PitA-like Piuptake system and a putative Na+-dependent Pitransporter and the genes involved in the metabolism of pyrophosphate and polyphosphate. In summary, a global, time-resolved picture of the response ofC. glutamicumto Pistarvation was obtained.
Unusual Integrase Gene Expression on the
clc
Genomic Island in
Pseudomonas
sp. Strain B13
Authors: Sentchilo V. , Ravatn R. , Werlen C. , Zehnder A. J. B. , van der Meer J. R.
Published: July 2003

An unusual type of gene expression from an integrase promoter was found in cultures of the bacterium
Pseudomonas
sp. strain B13. The promoter controls expression of the
intB13
integrase gene, which is present near the right end of a 105-kb conjugative genomic island (the
clc
element) encoding catabolism of aromatic compounds. The enzymatic activity of integrase IntB13 is essential for site-specific integration of the
clc
element into the bacterial host's chromosome. By creating transcription fusions between the
intB13
promoter and the
gfp
gene, we showed that integrase expression in strain B13 was inducible under stationary-phase conditions but, strangely, occurred in only a small proportion of individual bacterial cells rather than equally in the whole population. Integrase expression was significantly stimulated by growing cultures on 3-chlorobenzoate. High cell density, heat shock, osmotic shock, UV irradiation, and treatment with alcohol did not result in measurable integrase expression. The occurrence of the excised form of the
clc
element and an increase in the rates of
clc
element transfer in conjugation experiments correlated with the observed induction of the
intB13′-gfp
fusion in stationary phase and in the presence of 3-chlorobenzoate. This suggested that activation of the
intB13
promoter is the first step in stimulation of
clc
transfer. To our knowledge, this is the first report of a chlorinated compound's stimulating horizontal transfer of the genes encoding its very metabolism.
DNA Array-Based Transcriptional Analysis of Asporogenous, Nonsolventogenic
Clostridium acetobutylicum
Strains SKO1 and M5
Authors: Tomas Christopher A. , Alsaker Keith V. , Bonarius Hendrik P. J. , Hendriksen Wouter T. , Yang He , Beamish Jeffrey A. , Paredes Carlos J. , Papoutsakis Eleftherios T.
Published: July 2003

The large-scale transcriptional program of two
Clostridium acetobutylicum
strains (SKO1 and M5) relative to that of the parent strain (wild type [WT]) was examined by using DNA microarrays. Glass DNA arrays containing a selected set of 1,019 genes (including all 178 pSOL1 genes) covering more than 25% of the whole genome were designed, constructed, and validated for data reliability. Strain SKO1, with an inactivated
spo0A
gene, displays an asporogenous, filamentous, and largely deficient solventogenic phenotype. SKO1 displays downregulation of all solvent formation genes,
sigF
, and carbohydrate metabolism genes (similar to genes expressed as part of the stationary-phase response in
Bacillus subtilis
) but also several electron transport genes. A major cluster of genes upregulated in SKO1 includes
abrB
, the genes from the major chemotaxis and motility operons, and glycosylation genes. Strain M5 displays an asporogenous and nonsolventogenic phenotype due to loss of the megaplasmid pSOL1, which contains all genes necessary for solvent formation. Therefore, M5 displays downregulation of all pSOL1 genes expressed in the WT. Notable among other genes expressed more highly in WT than in M5 were
sigF
, several two-component histidine kinases,
spo0A
,
cheA
,
cheC
, many stress response genes,
fts
family genes, DNA topoisomerase genes, and central-carbon metabolism genes. Genes expressed more highly in M5 include electron transport genes (but different from those downregulated in SKO1) and several motility and chemotaxis genes. Most of these expression patterns were consistent with phenotypic characteristics. Several of these expression patterns are new or different from what is known in
B. subtilis
and can be used to test a number of functional-genomic hypotheses.
Characterization of Transcriptional Regulation ofShewanella frigidimarinaFe(III)-Induced FlavocytochromecReveals a Novel Iron-Responsive Gene Regulation System
Authors: Reyes-Ramirez Francisca , Dobbin Paul , Sawers Gary , Richardson David J.
Published: July 2003

The bacteriumShewanella frigidimarinacan grow anaerobically by utilizing Fe(III) as a respiratory electron acceptor. This results in the synthesis of a number of periplasmicc-type cytochromes, which are absent when the organism is grown in the absence of added Fe(III). One cytochrome, IfcA, is synthesized when Fe(III) is present as the sole respiratory electron acceptor or when it is present in combination with oxygen, fumarate, or nitrate. TheifcAgene was thus selected for a study of iron-responsive gene regulation of respiratory proteins inS. frigidimarina. The monocistronicifcAgene clusters with two other monocistronic genes,ifcO, encoding a putative outer membrane porin, andifcR, encoding a putative transcriptional regulator of the LysR superfamily. Analysis of transcription of all three genes under a range of growth conditions in the wild type and anifcRinsertion mutant and analysis of a strain that constitutively expressesifcRrevealed that iron regulation is exerted at the level ofifcRtranscription. In the presence of Fe(III) IfcR is synthesized and acts positively to regulate expression ofifcOandifcA. Control of Fe(III) respiration by this novel regulatory system differs markedly from Fur-mediated regulation of iron assimilation, in which Fur serves as an Fe(II)-activated repressor.
Initial Proteome Analysis of Model MicroorganismHaemophilus influenzaeStrain Rd KW20
Authors: Kolker Eugene , Purvine Samuel , Galperin Michael Y. , Stolyar Serg , Goodlett David R. , Nesvizhskii Alexey I. , Keller Andrew , Xie Tao , Eng Jimmy K. , Yi Eugene , Hood Leroy , Picone Alex F. , Cherny Tim , Tjaden Brian C. , Siegel Andrew F. , Reilly Thomas J. , Makarova Kira S. , Palsson Bernhard O. , Smith Arnold L.
Published: July 2003

The proteome ofHaemophilus influenzaestrain Rd KW20 was analyzed by liquid chromatography (LC) coupled with ion trap tandem mass spectrometry (MS/MS). This approach does not require a gel electrophoresis step and provides a rapidly developed snapshot of the proteome. In order to gain insight into the central metabolism ofH. influenzae, cells were grown microaerobically and anaerobically in a rich medium and soluble and membrane proteins of strain Rd KW20 were proteolyzed with trypsin and directly examined by LC-MS/MS. Several different experimental and computational approaches were utilized to optimize the proteome coverage and to ensure statistically valid protein identification. Approximately 25% of all predicted proteins (open reading frames) ofH. influenzaestrain Rd KW20 were identified with high confidence, as their component peptides were unambiguously assigned to tandem mass spectra. Approximately 80% of the predicted ribosomal proteins were identified with high confidence, compared to the 33% of the predicted ribosomal proteins detected by previous two-dimensional gel electrophoresis studies. The results obtained in this study are generally consistent with those obtained from computational genome analysis, two-dimensional gel electrophoresis, and whole-genome transposon mutagenesis studies. At least 15 genes originally annotated as conserved hypothetical were found to encode expressed proteins. Two more proteins, previously annotated as predicted coding regions, were detected with high confidence; these proteins also have close homologs in related bacteria. The direct proteomics approach to studying protein expression in vivo reported here is a powerful method that is applicable to proteome analysis of any (micro)organism.
Identification of Upstream Sequences Essential for Activation of a Bacteriophage P2 Late Promoter
Authors: Christie Gail E. , Anders Douglas L. , McAlister Victor , Goodwin Tina S. , Julien Bryan , Calendar Richard
Published: July 2003

We have carried out a mutational scan of the upstream region of the bacteriophage P2
FETUD
late operon promoter, P
F
, which spans an element of hyphenated dyad symmetry that is conserved among all six of the P2 and P4 late promoters. All mutants were assayed for activation by P4 Delta in vivo, by using a
lacZ
reporter plasmid, and a subset of mutants was assayed in vitro for Delta binding. The results confirm the critical role of the three complementary nucleotides in each half site of the upstream element for transcription factor binding and for activation of transcription. A trinucleotide DNA recognition site is consistent with a model in which these transcription factors bind via a zinc finger motif. The mutational scan also led to identification of the −35 region of the promoter. Introduction of a σ
70
−35 consensus sequence resulted in increased constitutive expression, which could be further stimulated by Delta. These results indicate that activator binding to the upstream region of P2 late promoters compensates in part for poor σ
70
contacts and helps to recruit RNA polymerase holoenzyme.
Competition between MutY and Mismatch Repair at A · C Mispairs In Vivo
Authors: Kim Mandy , Huang Tiffany , Miller Jeffrey H.
Published: July 2003

We show that the MutY protein competes with the MutS-dependent mismatch repair system to process at least some A · C mispairs in vivo, converting them to G · C pairs. In the presence of an increased dCTP pool resulting from the loss of nucleotide diphosphate kinase, the frequency of A · T→G · C transitions at a hot spot in the
rpoB
gene is 30-fold lower in a MutY-deficient derivative than in the wild type.
Using a DNA Microarray To Investigate the Distribution of Insect Virulence Factors in Strains of
Photorhabdus
Bacteria
Authors: Marokhazi Judit , Waterfield Nicholas , LeGoff Gaelle , Feil Edward , Stabler Richard , Hinds Jason , Fodor Andras , ffrench-Constant Richard H.
Published: July 2003

Photorhabdus
is an insect-pathogenic bacterium in which oral toxicity to insects is found in two distinct taxonomic groups. Using a DNA microarray and comparative genomics, we show that oral toxicity is associated with toxin complex genes
tcaABC
and that this locus can be mobilized or deleted within different strains.
Cytosine Methylation by the
Sua
I Restriction-Modification System: Implications for Genetic Fidelity in a Hyperthermophilic Archaeon
Authors: Grogan Dennis W.
Published: July 2003

5-Methylcytosine in chromosomal DNA represents a potential source of frequent spontaneous mutation for hyperthermophiles. To determine the relevance of this threat for the archaeon
Sulfolobus acidocaldarius
, the mode of GGCC methylation by its restriction-modification system,
Sua
I, was investigated. Distinct isoschizomers of the
Sua
I endonuclease were used to probe the methylation state of GGCC in native
S. acidocaldarius
DNA. In addition, the methylation sensitivity of the
Sua
I endonuclease was determined with synthetic oligonucleotide substrates and modified natural DNAs. The results show that the
Sua
I system uses
N
4
methylation to block cleavage of its recognition site, thereby avoiding the creation of G · T mismatches by spontaneous deamination at extremely high temperature.
Methanococcus jannaschii
Coenzyme F
420
Analogs Contain a Terminal α-Linked Glutamate
Authors: Graupner Marion , White Robert H.
Published: July 2003

Analyses of the F
420
s present in
Methanococcus jannaschii
have shown that these cells contain a series of γ-glutamyl-linked F
420
s capped with a single, terminal α-linked
l
-glutamate. The predominant form of F
420
was designated as α-F
420
-3 and represented 86% of the F
420
s in these cells. Analyses of
Methanosarcina thermophila
,
Methanosarcina barkeri
,
Methanobacterium thermoautotrophicum
,
Archaeoglobus fulgidus
, and
Mycobacterium smegmatis
showed that they contained only γ-glutamyl-linked F
420
s.
Quantum Spin Nematic States in Bose–Einstein Condensates
Authors: Zhou Fei
Published: July 2003

We review some recent results on discrete symmetries and topological order in spinor Bose–Einstein condensates (BECs) of 23Na. For spin one bosons with two-body scatterings dominated by a total spin equal to two channel, the BECs are in quantum spin nematic states at a low density limit. We study spin correlations in condensates at different limits and analyze hidden symmetries using a non-perturbative approach developed recently. Furthermore we investigate the influence of hidden Z2 symmetries and U(1) quantum orders in symmetry partially restored states, particularly the effects on topological excitations.
Quantum Dynamics and Entropy in a Single-Cooper-Pair Box with a Single-Mode Cavity Field
Authors: Zhang Meng , Zou Jian , Shao Bin
Published: July 2003

We consider a single-Cooper-pair box biased by a classical voltage and also irradiated by a single-mode quantized field. We assume that the box is initially in a mixed state, and investigate the quantum dynamics of the Cooper-pair box and show that the collapse and revival phenomenon can exist in this system. We also study the quantum entropy of the single-Cooper-pair box and discuss the effects of the different parameters on this quantum entropy. We find that the box, which is initially in a mixed state, may evolve into an almost pure state.
Effects of Temperature on the Emulsification in Surfactant-Water-Oil Systems
Authors: Yuan Yin-Quan , Zou Xian-Wu , Xiong Ping-Fan
Published: July 2003

The effect of temperature on the emulsification has been investigated by discontinuous molecular dynamic simulation. When a large oil drop is put in water, on one hand the mixing entropy makes it divide into small oil drops; on the other hand the interactions among particles drives the small oil drops fowards aggregation. The evolution of the mean size of oil drops obeys the exponential delay law. There exist an active temperature, at which, the addition of surfactants has obvious effect on the emulsification. The surfactants with low HLB value (e.g. H1T3) make the dispersity of emulsion decrease, and the surfactants with high HLB value (e.g. H2T2and H3T1) make a contribution to increase the dispersity of emulsion.
An Endangered Living System
Authors: Hough Robbin R.
Published: July 2003

The high flow rates of the connecting channel between Lake Huron and Lake Erie allow the channel to absorb massive quantities of chemicals and waste materials without an apparent immediate impact. A study carried out in the late 1980s by the USEPA/Environment Canada pointed to the potentially profound impacts on downstream living systems of continuing the uses that then prevailed. The paper reviews the major changes which have taken place since the earlier study was completed and outlines pieces of the scientific case to be made for needed changes in the ways in which the Great Lakes are being managed.
Equilibrium Analysis of a Mathematical Model for the Spread of AIDS in a Two Sex Population with Mixing Constraints
Authors: Doyle Murray , Greenhalgh David , Blythe Steve
Published: July 2003

For a mathematical model for the spread of HIV by sexual transmission in a heterosexual population we analyse the existence and stability of equilibrium solutions. The model is designed to investigate the effects of a fundamental constraint in any social/sexual mixing process for heterogeneous populations. The group contact constraint conserves the number of new sexual partnerships formed per unit time between the sexes, and will have at least a quantitative influence on the dynamics of the model. The analysis has been carried out for general and specific forms of the sexual activity rates (the mean number of sexual partners per unit time for a typical individual). In general we define a threshold parameter R0, the Reproductive Number, which is a key determinant of the behaviour of the model. We show that in general if R0>1 there is at least one endemic equilibrium. The specific cases of a dominance sexual activity rate and proportional sexual activity rates are discussed in more detail. Multiple endemic equilibria can occur for the former but not the latter.
Manipulating Face Gender
Authors: Deffenbacher Kenneth A. , Hendrickson Cheryl , O'Toole Alice J. , Huff David P. , Abdi Hervé
Published: July 2003

Previous research has shown that faces coded as pixel-based images may be constructed from an appropriately weighted combination of statistical "features" (eigenvectors) which are useful for discriminating members of a learned set of images. We have shown previously that two of the most heavily weighted features are important in predicting face gender. Using a simple computational model, we adjusted weightings of these features in more masculine and more feminine directions for both male and female adult Caucasian faces. In Experiment 1, cross-gender face image alterations (e.g., feminizing male faces) reduced both gender classification speed and accuracy for young adult Caucasian observers, whereas same-gender alterations (e.g., masculinizing male faces) had no effect as compared to unaltered controls. Effects on femininity-masculinity ratings mirrored those obtained on gender classification speed and accuracy. We controlled statistically for possible effects of image distortion incurred by our gender manipulations. In Experiment 2 we replicated the same pattern of accuracy data. Combined, these data indicate the psychological relevance of the features derived from the computational model. Despite having different effects on the ease of gender classification, neither sort of gender alteration negatively impacted face recognition (Experiment 3), yielding evidence for a model of face recognition wherein gender and familiarity processing proceed in parallel.
Effects of Noise on Coordination of Nonlinear Biochemical Systems
Authors: Liu Junli
Published: July 2003

Effects of noisy fluctuations in environment on coordination of nonlinear biochemical systems have been analyzed both theoretically and numerically. Once noise induces dynamical changes in a nonlinear biochemical system, response of flux to noisy fluctuations depends on both the dynamics of the system, the nature of the superimposed noise and the values of kinetical parameters, while a steady-state flux in the absence of noise may only depend on the values of kinetical parameters. For a branched biochemical system, noise may induce significant redistribution of flux among the branched reactions. Furthermore, noise may destroy coordination of a nonlinear biochemical system, when it cannot accommodate noise-induced changes. An empirical method has been suggested to determine whether coordination of a biochemical system is destroyed by environmental noise, and a general approach for studying coordination of biochemical systems under noisy fluctuations has also been presented. The theoretical results suggest that studies on coordination and homoeostasis of nonlinear biochemical systems must take their nonlinearities into account. The implications of the theoretical results for understanding flux control, homoeostasis and coordination of nonlinear biochemical systems in the presence of noise have been discussed.
Bioeconomic Modelling of a Single Species Fishery with Gompertz Law of Growth
Authors: Pradhan T. , Chaudhuri K. S.
Published: July 2003

A single species fishery model has been developed using the Gompertz law of population growth and the CPUE (Catch-per-unit-effort) hypothesis. The dynamical and the bionomic steady states were determined and their natures were examined from the biological as well as economic view points. The optimal harvest policy is discussed by taking the fishing effort as a dynamic control variable. The results are compared with those of the Schaefer model [10].