bluuebunny/crossref_metadata_2025 huggingface dataset:
Scientific discovery of the function of ear in the light of material property
Authors: Paul Hari S. , Kumaresan M.
Published: July 2002

Piezoelectricity is conversion of mechanical energy to electric energy and vice versa. This property exhibits in noncentrocymetric materials. Bone is well-known piezoelectric material in living body. Eardrum is connected with bones (malleus, incus, stapes, and bony cochlea). Cochlea is snail-shaped and filled with fluid and hair cells (human electrodes). Fluid is centrocymetric; hence, it is nonpiezoelectric material. Acoustic pressure on eardrum sets mechanical energy to these bones. Bones convert mechanical energy to electric polarization, which is direct piezoelectric property. Electric charges generated in bones are transmitted through fluid as ±ions (like a car battery charger) and picked up by −/+ hair cells and auditory nerves for transmission to brain. Transmissions of ±charges through fluid generate movement of fluid. Cochlea replacement is required when hair cells in cochlea lose their power to transmit charges. Vocal cord surrounded by cricoid and arytenoid cartilages is known as vocal box/larynx. Larynx transforms pulse energy to sound energy (converse piezoelectric property). Vocal cord narrowing and opening its air passage from lungs can also produce sound. Present concept of ear function contradicts majority of doctor’s view, that is, fluid in cochlea transforms sound (mechanical) energy to electric energy, which is untrue.
Pseudomonas
-
Candida
Interactions: An Ecological Role for Virulence Factors
Authors: Hogan Deborah A. , Kolter Roberto
Published: July 2002

Bacterial-fungal interactions have great environmental, medical, and economic importance, yet few have been well characterized at the molecular level. Here, we describe a pathogenic interaction between
Pseudomonas aeruginosa
and
Candida albicans
, two opportunistic pathogens.
P. aeruginosa
forms a dense biofilm on
C. albicans
filaments and kills the fungus. In contrast,
P. aeruginosa
neither binds to nor kills yeast-form
C. albicans
. Several
P. aeruginosa
virulence factors that are important in disease are involved in the killing of
C. albicans
filaments. We propose that many virulence factors studied in the context of human infection may also have a role in bacterial-fungal interactions.
Sequence-Specific Molecular Lithography on Single DNA Molecules
Authors: Keren Kinneret , Krueger Michael , Gilad Rachel , Ben-Yoseph Gdalyahu , Sivan Uri , Braun Erez
Published: July 2002

Recent advances in the realization of individual molecular-scale electronic devices emphasize the need for novel tools and concepts capable of assembling such devices into large-scale functional circuits. We demonstrated sequence-specific molecular lithography on substrate DNA molecules by harnessing homologous recombination by RecA protein. In a sequence-specific manner, we patterned the coating of DNA with metal, localized labeled molecular objects and grew metal islands on specific sites along the DNA substrate, and generated molecularly accurate stable DNA junctions for patterning the DNA substrate connectivity. In our molecular lithography, the information encoded in the DNA molecules replaces the masks used in conventional microelectronics, and the RecA protein serves as the resist. The molecular lithography works with high resolution over a broad range of length scales from nanometers to many micrometers.
50 Million Years of Genomic Stasis in Endosymbiotic Bacteria
Authors: Tamas Ivica , Klasson Lisa , Canbäck Björn , Näslund A. Kristina , Eriksson Ann-Sofie , Wernegreen Jennifer J. , Sandström Jonas P. , Moran Nancy A. , Andersson Siv G. E.
Published: July 2002

Comparison of two fully sequenced genomes of
Buchnera aphidicola
, the obligate endosymbionts of aphids, reveals the most extreme genome stability to date: no chromosome rearrangements or gene acquisitions have occurred in the past 50 to 70 million years, despite substantial sequence evolution and the inactivation and loss of individual genes. In contrast, the genomes of their closest free-living relatives,
Escherichia coli
and
Salmonella
spp., are more than 2000-fold more labile in content and gene order. The genomic stasis of
B. aphidicola
, likely attributable to the loss of phages, repeated sequences, and
recA
, indicates that
B. aphidicola
is no longer a source of ecological innovation for its hosts.
Evolution and Development of Sex Differences in Cooperative Behavior in Meerkats
Authors: Clutton-Brock T. H. , Russell A. F. , Sharpe L. L. , Young A. J. , Balmforth Z. , McIlrath G. M.
Published: July 2002

In cooperatively breeding birds, where helpers of both sexes assist with the provisioning and upbringing of offspring who are not their own, males tend to contribute more than females to rearing young. This sex difference has been attributed to paternity uncertainty, but could also occur because males contribute more where they are likely to remain and breed in their group of origin. In contrast to most birds, female meerkats (
Suricata suricatta
) are more likely to breed in their natal group than males. We show that female meerkat helpers contribute more to rearing young than males and that female helpers feed female pups more frequently than males. Our results suggest that sex differences in cooperative behavior are generated by sex differences in philopatry and occur because females derive greater direct benefits than males from raising recruits to their natal group. These findings support the view that direct, mutualistic benefits are important in the evolution of specialized cooperative behavior.
Serotonin Transporter Genetic Variation and the Response of the Human Amygdala
Authors: Hariri Ahmad R. , Mattay Venkata S. , Tessitore Alessandro , Kolachana Bhaskar , Fera Francesco , Goldman David , Egan Michael F. , Weinberger Daniel R.
Published: July 2002

A functional polymorphism in the promoter region of the human serotonin transporter gene (
SLC6A4
) has been associated with several dimensions of neuroticism and psychopathology, especially anxiety traits, but the predictive value of this genotype against these complex behaviors has been inconsistent. Serotonin [5- hydroxytryptamine, (5-HT)] function influences normal fear as well as pathological anxiety, behaviors critically dependent on the amygdala in animal models and in clinical studies. We now report that individuals with one or two copies of the short allele of the serotonin transporter (5-HTT) promoter polymorphism, which has been associated with reduced 5-HTT expression and function and increased fear and anxiety-related behaviors, exhibit greater amygdala neuronal activity, as assessed by BOLD functional magnetic resonance imaging, in response to fearful stimuli compared with individuals homozygous for the long allele. These results demonstrate genetically driven variation in the response of brain regions underlying human emotional behavior and suggest that differential excitability of the amygdala to emotional stimuli may contribute to the increased fear and anxiety typically associated with the short
SLC6A4
allele.
Spontaneous Organization of Single CdTe Nanoparticles into Luminescent Nanowires
Authors: Tang Zhiyong , Kotov Nicholas A. , Giersig Michael
Published: July 2002

Nanoparticles of CdTe were found to spontaneously reorganize into crystalline nanowires upon controlled removal of the protective shell of organic stabilizer. The intermediate step in the nanowire formation was found to be pearl-necklace aggregates. Strong dipole-dipole interaction is believed to be the driving force of nanoparticle self-organization. The linear aggregates subsequently recrystallized into nanowires whose diameter was determined by the diameter of the nanoparticles. The produced nanowires have high aspect ratio, uniformity, and optical activity. These findings demonstrate the collective behavior of nanoparticles as well as a convenient, simple technique for production of one-dimensional semiconductor colloids suitable for subsequent processing into quantum-confined superstructures, materials, and devices.
A Tropical Rainforest in Colorado 1.4 Million Years After the Cretaceous-Tertiary Boundary
Authors: Johnson Kirk R. , Ellis Beth
Published: July 2002

An extremely diverse lower Paleocene (64.1 million years ago) fossil leaf site from Castle Rock, Colorado, contains fossil litter that is similar to the litter of extant equatorial rainforests. The presence of a high-diversity tropical rainforest is unexpected, because other Paleocene floras are species-poor, a feature generally attributed to the Cretaceous-Tertiary (K-T) extinction. The site occurs on the margin of the Denver Basin in synorogenic sedimentary rocks associated with the rise of the Laramide Front Range. Orographic conditions caused by local topography, combined with equable climate, appear to have allowed for the establishment of rainforests within 1.4 million years of the K-T boundary.
Generation of Self-Incompatible
Arabidopsis thaliana
by Transfer of Two
S
Locus Genes from
A. lyrata
Authors: Nasrallah Mikhail E. , Liu Pei , Nasrallah June B.
Published: July 2002

Transitions from cross-fertilizing to self-fertilizing mating systems have occurred frequently in natural and domesticated plant populations, but the underlying genetic causes are unknown. We show that gene transfer of the stigma receptor kinase SRK and its pollen-borne ligand SCR from one
S-
locus haplotype of the self-incompatible and cross-fertilizing
Arabidopsis lyrata
is sufficient to impart self-incompatibility phenotype in self-fertile
Arabidopsis thaliana
, which lacks functional orthologs of these genes. This successful complementation demonstrates that the signaling cascade leading to inhibition of self-related pollen was maintained in
A. thaliana.
Analysis of self-incompatibility will be facilitated by the tools available in this species.
Nitrate Controls on Iron and Arsenic in an Urban Lake
Authors: Senn David B. , Hemond Harold F.
Published: July 2002

Aquatic ecosystems are often contaminated by multiple substances. Nitrate, a common aquatic pollutant, strongly influenced the cycling of arsenic (As) under anoxic conditions in urban Upper Mystic Lake (Massachusetts, USA) by oxidizing ferrous iron [Fe(II)] to produce As-sorbing particulate hydrous ferric oxides and causing the more oxidized As(V), which is more particle-reactive than As(III) under these conditions, to dominate. This process is likely to be important in many natural waters.
The Function of the Cranial Crest and Jaws of a Unique Pterosaur from the Early Cretaceous of Brazil
Authors: Kellner Alexander W. A. , Campos Diogenes de Almeida
Published: July 2002

The discovery of a previously undescribed pterosaur,
Thalassodromeus sethi
, yields information on the function of cranial crests and the feeding strategy developed by these extinct flying reptiles. The material consists of a large skull (length: 1420 millimeters, including the crest) with a huge bony crest that was well irrigated by blood vessels and may have been used for regulation of its body temperature. The rostrum consists of two bladelike laminae, the arrangement of which is analogous to the condition found in the bird
Rynchops
, which skims over the water to catch food, indicating that
T
.
sethi
also may have been a skimmer.
New Vines on Old Roots
Authors: Garrett Merrill
Published: July 2002

Foundations of Language
Brain, Meaning, Grammar, Evolution. Ray Jackendoff. Oxford University Press, New York, 2002. 497 pp. $40, £25. ISBN 0-19-827012-7.

Building on developments in linguistics over the past half century, Jackendoff offers an interpretation of "parallel architecture" to explain how the brain stores and processes language.
A Role for Peroxisomes in Photomorphogenesis and Development of
Arabidopsis
Authors: Hu Jianping , Aguirre Maria , Peto Charles , Alonso José , Ecker Joseph , Chory Joanne
Published: July 2002

The nuclear protein DET1 is a central repressor of photomorphogenesis in plants. We have identified the molecular lesion in
ted3
, a mutation that dominantly suppresses the phenotypes of
det1-1
.
TED3
encodes a peroxisomal protein (AtPex2p) essential for
Arabidopsis
growth. Developmental defects and the abnormal expression of many genes in
det1
are rescued by
ted3
.
ted3
also partially suppresses another pleiotropic de-etiolated mutant
cop1
. Thus, peroxisomes, whose functions are still largely unexplored, play a key role in a photomorphogenetic pathway negatively regulated by the DET1 and COP proteins.
Probing Oxygen Motion in Disordered Anionic Conductors with
17
O and
51
V MAS NMR Spectroscopy
Authors: Kim Namjun , Grey Clare P.
Published: July 2002

Identification of the local environments of the ions in a solid-state electrolyte that contribute to the ionic conductivity or remain trapped in the lattice represents a challenge for many experimental probes of structure. We show that high-resolution
17
O magic angle spinning nuclear magnetic resonance (MAS NMR) spectra may be obtained even from the highly disordered, layered materials α-Bi
4
V
2
O
11
and γ-Bi
4
V
1.7
Ti
0.3
O
10.85
, in which the different oxide sites in the lattice may be distinguished. The sites responsible for anionic conduction were determined directly from the variable-temperature
17
O NMR spectra, and correlation times for motion were estimated. Double-resonance
17
O/
51
V NMR methods were used as confirmation of the assignments of the resonances and as a second experimental probe of motion that is sensitive to mobility involving oxide ion hops between the same crystallographic sites.
Consequences of Raising Cane
Authors: Cañizares-Esguerra Jorge
Published: July 2002

States of Nature
Science, Agriculture, and Environment in the Spanish Caribbean, 1760-1940. Stuart McCook. University of Texas Press, Austin, 2002. 215 pp. $50. ISBN 0-292-75256-3. Paper, $22.95. ISBN 0-292-75257-1.

Examining the history of the agricultural and botanical sciences in Venezuela, Puerto Rico, Cuba, Columbia, and Costa Rica, McCook concludes that growers and governments turned to science to help alleviate environmental and economic stresses without having to abandon their goals of export-led growth.
Genetic Divergence of Human Immunodeficiency Virus Type 1 Ethiopian Clade C Reverse Transcriptase (RT) and Rapid Development of Resistance against Nonnucleoside Inhibitors of RT
Authors: Loemba Hugues , Brenner Bluma , Parniak Michael A. , Ma'ayan Shlomo , Spira Bonnie , Moisi Daniela , Oliveira Maureen , Detorio Mervi , Wainberg Mark A.
Published: July 2002

We sequenced and phylogenetically analyzed the reverse transcriptase (RT) region of five human immunodeficiency virus type 1 isolates from treatment-naive Ethiopian émigrés to Israel. Heteroduplex mobility assays were performed to confirm the clade C status of
env
genomic regions. The RT sequences showed that the strains clustered phylogenetically with clade C viruses, and a KVEQ-specific motif of silent mutations (amino acids 65, 106, 138, and 161, respectively) at resistance sites was present in the polymerase region of all studied Ethiopian isolates and subtype C reference strains. In addition, many other silent mutations were observed in the clade C viruses at various resistance sites. In general, the Ethiopian isolates were more closely related genotypically to a clade C reference strain from Botswana (southern Africa) than to previously sequenced Ethiopian reference strains. Genotypic analysis showed that two Ethiopian isolates naturally harbored the mutations K70R and G190A associated with resistance to ZDV and nonnucleoside reverse transcriptase inhibitors, respectively. Phenotypic assays revealed that the K70R substitution in this context did not reduce susceptibility to ZDV, whereas the G190A substitution resulted in high-level resistance to nevirapine (NVP). Moreover, variants resistant to NVP, delavirdine (DLV), and efavirenz (EFV) were more rapidly selected at lower drug doses culture with clade C than with clade B wild-type isolates. In the case of subtype C, selection with NVP and/or EFV led to the appearance of several previously unseen mutations in RT, i.e., V106M and S98I, as well as other mutations that have been previously reported (e.g., K103N, V106A, V108I, and Y181C). After selection with DLV, a polymorphism, A62A, initially observed in the Ethiopian isolate 4762, mutated to A62V; the latter is a secondary substitution associated with multidrug resistance against nucleoside RT inhibitors. Phenotypic analysis of clade C mutants selected against NVP, DLV, and EFV revealed broad cross-resistance, particularly in regard to NVP and DLV. These findings suggest that RT genotypic diversity may influence the emergence of drug resistance.
Enzymes Associated with Reductive Activation and Action of Nitazoxanide, Nitrofurans, and Metronidazole in
Helicobacter pylori
Authors: Sisson Gary , Goodwin Avery , Raudonikiene Ausra , Hughes Nicky J. , Mukhopadhyay Asish K. , Berg Douglas E. , Hoffman Paul S.
Published: July 2002

Nitazoxanide (NTZ) is a redox-active nitrothiazolyl-salicylamide prodrug that kills
Helicobacter pylori
and also many anaerobic bacterial, protozoan, and helminthic species. Here we describe development and use of a spectrophotometric assay, based on nitroreduction of NTZ at 412 nm, to identify
H. pylori
enzymes responsible for its activation and mode of action. Three enzymes that reduce NTZ were identified: two related NADPH nitroreductases, which also mediate susceptibility to metronidazole (MTZ) (RdxA and FrxA), and pyruvate oxidoreductase (POR). Recombinant His-tagged RdxA, FrxA, and POR, overexpressed in nitroreductase-deficient
Escherichia coli
, each rapidly reduced NTZ, whereas only FrxA and to a lesser extent POR reduced nitrofuran substrates (furazolidone, nitrofurantoin, and nitrofurazone). POR exhibited no MTZ reductase activity either in extracts of
H. pylori
or following overexpression in
E. coli
; RdxA exhibited no nitrofuran reductase activity, and FrxA exhibited no MTZ reductase activity. Analysis of mutation to rifampin resistance (Rif
r
) indicated that NTZ was not mutagenic and that nitrofurans were only weakly mutagenic. Alkaline gel DNA electrophoresis indicated that none of these prodrugs caused DNA breakage. In contrast, MTZ caused DNA damage and was strongly mutagenic. We conclude that POR, an essential enzyme, is responsible for most or all of the bactericidal effects of NTZ against
H. pylori
. While loss-of-function mutations in
rdxA
and
frxA
produce a Mtz
r
phenotype, they do not contribute much to the innate susceptibility of
H. pylori
to NTZ or nitrofurans.
Novel Class 1 Integron (InS21) Carrying
bla
CTX-M-2
in
Salmonella enterica
Serovar Infantis
Authors: Di Conza José , Ayala Juan A. , Power Pablo , Mollerach Marta , Gutkind Gabriel
Published: July 2002

The genetic organization of the region coding for CTX-M-2 in
Salmonella enterica
serovar Infantis was determined by PCR mapping. This gene seems to have been mobilized from the
Kluyvera ascorbata
chromosome to a complex
sulI
-type integron, similar to In6 and In7.
In Vivo Activity of Posaconazole againstMucorspp. in an Immunosuppressed-Mouse Model
Authors: Sun Qiu N. , Najvar Laura K. , Bocanegra Rosie , Loebenberg David , Graybill John R.
Published: July 2002

The in vivo activities of posaconazole, itraconazole, and amphotericin B in neutropenic mice with zygomycosis were compared. The in vitro MICs of posaconazole and itraconazole for the strains ofMucorspp. used in this study ranged from 0.125 to 8 μg/ml and 0.25 to 8 μg/ml, respectively. The in vitro MIC range for amphotericin B is 0.125 to 0.25 μg/ml. At twice-daily doses of ≥15 mg/kg of body weight, posaconazole prolonged the survival of the mice and reduced tissue burden.
Hexapeptide Derivatives of Glycopeptide Antibiotics: Tools for Mechanism of Action Studies
Authors: Allen Norris E. , LeTourneau Deborah L. , Hobbs Joe N. , Thompson Richard C.
Published: July 2002

Hexapeptide (des-
N
-methylleucyl) derivatives of LY264826 were prepared in order to examine further the role of N-substituted hydrophobic side chains in defining the mechanisms of action of semisynthetic glycopeptide antibiotics. The hexapeptide of LY264826 binds to the cell wall intermediate analog
l
-Lys-
d
-Ala-
d
-Ala with a 100-fold lower affinity than LY264826 and inhibits
Micrococcus luteus
almost 200-fold more poorly than LY264826 does. Alkylation of the 4-epi-vancosamine moiety of the disaccharide significantly enhanced the antibacterial activity of the hexapeptide. Alkylation did not affect the binding affinity for
d
-alanyl-
d
-alanine residues; however, it did enhance dimerization 7,000-fold and enhanced binding to bacterial membrane vesicles noticeably compared with the levels of dimerization and binding for the unsubstituted hexapeptide. The findings from this study complement those presented in an earlier report (N. E. Allen, D. L. LeTourneau, and J. N. Hobbs, Jr., J. Antibiot. 50:677-684, 1997) and are consistent with the conclusion that the enhanced antibacterial activities of semisynthetic glycopeptide antibiotics derive from the ability of the hydrophobic side chain to markedly affect both dimerization and binding to bacterial membranes.
N-Arylsulfonyl Hydrazones as Inhibitors of IMP-1 Metallo-β-Lactamase
Authors: Siemann Stefan , Evanoff Darryl P. , Marrone Laura , Clarke Anthony J. , Viswanatha Thammaiah , Dmitrienko Gary I.
Published: July 2002

Members of a family ofN-arylsulfonyl hydrazones have been identified as novel inhibitors of IMP-1, a metallo-β-lactamase of increasing prevalence. Structure-activity relationship studies have indicated a requirement for bulky aromatic substituents on each side of the sulfonyl hydrazone backbone for these compounds to serve as efficient inhibitors of IMP-1. Molecular modeling has provided insight into the structural basis for the anti-metallo-β-lactamase activity exhibited by this class of compounds.
Distribution of
mef
(A) in Gram-Positive Bacteria from Healthy Portuguese Children
Authors: Luna Vicki A. , Heiken Marc , Judge Kathleen , Ulep Catherine , Van Kirk Nicole , Luis Henrique , Bernardo Mario , Leitao Jose , Roberts Marilyn C.
Published: July 2002

We screened 615 gram-positive isolates from 150 healthy children for the presence of the
erm
(A),
erm
(B),
erm
(C),
erm
(F), and
mef
(A) genes. The
mef
(A) genes were found in 20 (9%) of the macrolide-resistant isolates, including
Enterococcus
spp.,
Staphylococcus
spp., and
Streptococcus
spp. Sixteen of the 19 gram-positive isolates tested carried the other seven open reading frames (ORFs) described in Tn
1207.1
, a genetic element carrying
mef
(A) recently described in
Streptococcus pneumoniae
. The three
Staphylococcus
spp. did not carry
orf1
to
orf3
. A gram-negative
Acinetobacter junii
isolate also carried the other seven ORFs described in Tn
1207.1.
A
Staphylococcus aureus
isolate, a
Streptococcus intermedius
isolate, a
Streptococcus
sp. isolate, and an
Enterococcus
sp. isolate had their
mef
(A) genes completely sequenced and showed 100% identity at the DNA and amino acid levels with the
mef
(A) gene from
S. pneumoniae
.
In Vitro Evaluation of AZD2563, a Novel Oxazolidinone, against 603 Recent Staphylococcal Isolates
Authors: Anderegg Tamara R. , Biedenbach Douglas J. , Jones Ronald N.
Published: July 2002

AZD2563, a novel oxazolidinone, and a selection of comparator drugs that included linezolid, erythromycin, clindamycin, quinolones, and gentamicin were tested against 384
Staphylococcus aureus
(176 oxacillin-resistant
S. aureus
[ORSA]) and 219 coagulase-negative staphylococci (CoNS; 162 oxacillin resistant) by reference microdilution (all strains) and agar dilution (30 strains) methods. The following results were noted for AZD2563. (Note that, for comparison only, a breakpoint of ≤4 μg/ml [the breakpoint of linezolid] was used for this study, although a susceptibility breakpoint for AZD2563 has not been determined.) For
S. aureus
, the MIC at which 50% of the isolates tested are inhibited (MIC
50
) was 1 μg/ml, the MIC
90
was 2 μg/ml, and the percent susceptibility was 100%. For CoNS, the MIC
50
was 0.5 μg/ml, the MIC
90
was 1 μg/ml, and the percent susceptibility was 100%. ORSA and OR-CoNS strains were equally inhibited by AZD2563 and linezolid. AZD2563 demonstrated antistaphylococcal activity comparable to that of linezolid.
Activities of ABT-773 against Microaerophilic and Fastidious Organisms
Authors: Finegold Sydney M. , Molitoris Denise , Phan V. T. , Vaisanen M.-L. , Wexler Hannah M.
Published: July 2002

ABT-773 was tested against 317 fastidious isolates; it inhibited 99% of organisms at a concentration of 4.0 μg/ml. With ampicillin-sulbactam and levofloxacin, only 2 and 6% of these strains, respectively, were resistant at the breakpoint. With clindamycin, penicillin G, and metronidazole, 22, 26, and 58% of the strains, respectively, were resistant.
Members of the Family
Comamonadaceae
as Primary Poly(3-Hydroxybutyrate-co-3-Hydroxyvalerate)-Degrading Denitrifiers in Activated Sludge as Revealed by a Polyphasic Approach
Authors: Khan Shams Tabrez , Horiba Yoko , Yamamoto Masamitsu , Hiraishi Akira
Published: July 2002

The distribution and phylogenetic affiliations of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV)-degrading denitrifying bacteria in activated sludge were studied by a polyphasic approach including culture-independent biomarker and molecular analyses as well as cultivation methods. A total of 23 strains of PHBV-degrading denitrifiers were isolated from activated sludges from different sewage treatment plants. 16S ribosomal DNA (rDNA) sequence comparisons showed that 20 of the isolates were identified as members of the family
Comamonadaceae
, a major group of β-
Proteobacteria.
When the sludges from different plants were acclimated with PHBV under denitrifying conditions in laboratory scale reactors, the nitrate removal rate increased linearly during the first 4 weeks and reached 20 mg NO
3
−
-N h
−1
g of dry sludge
−1
at the steady state. The bacterial-community change in the laboratory scale sludges during the acclimation was monitored by rRNA-targeted fluorescence in situ hybridization and quinone profiling. Both approaches showed that the population of β-
Proteobacteria
in the laboratory sludges increased sharply during acclimation regardless of their origins. 16S rDNA clone libraries were constructed from two different acclimated sludges, and a total of 37 clones from the libraries were phylogenetically analyzed. Most of the 16S rDNA clones were grouped with members of the family
Comamonadaceae
. The results of our polyphasic approach indicate that β-
Proteobacteria
, especially members of the family
Comamonadaceae
, are primary PHBV-degrading denitrifiers in activated sludge. Our data provide useful information for the development of a new nitrogen removal system with solid biopolymer as an electron donor.
Process and Metabolic Strategies for Improved Production of
Escherichia coli
-Derived 6-Deoxyerythronolide B
Authors: Pfeifer Blaine , Hu Zhihao , Licari Peter , Khosla Chaitan
Published: July 2002

Recently, the feasibility of using
Escherichia coli
for the heterologous biosynthesis of complex polyketides has been demonstrated. In this report, the development of a robust high-cell-density fed-batch procedure for the efficient production of complex polyketides is described. The effects of various physiological conditions on the productivity and titers of 6-deoxyerythronolide B (6dEB; the macrocyclic core of the antibiotic erythromycin) in recombinant cultures of
E. coli
were studied in shake flask cultures. The resulting data were used as a foundation to develop a high-cell-density fermentation procedure by building upon procedures reported earlier for recombinant protein production in
E. coli
. The fermentation strategy employed consistently produced ∼100 mg of 6dEB per liter, whereas shake flask conditions generated between 1 and 10 mg per liter. The utility of an accessory thioesterase (TEII from
Saccharopolyspora erythraea
) for enhancing the productivity of 6dEB in
E. coli
was also demonstrated (increasing the final titer of 6dEB to 180 mg per liter). In addition to reinforcing the potential for using
E. coli
as a heterologous host for wild-type- and engineered-polyketide biosynthesis, the procedures described in this study may be useful for the production of secondary metabolites that are difficult to access by other routes.
Identification of anopd(Organophosphate Degradation) Gene in anAgrobacteriumIsolate
Authors: Horne Irene , Sutherland Tara D. , Harcourt Rebecca L. , Russell Robyn J. , Oakeshott John G.
Published: July 2002

We isolated a bacterial strain,Agrobacterium radiobacterP230, which can hydrolyze a wide range of organophosphate (OP) insecticides. A gene encoding a protein involved in OP hydrolysis was cloned fromA. radiobacterP230 and sequenced. This gene (calledopdA) had sequence similarity toopd, a gene previously shown to encode an OP-hydrolyzing enzyme inFlavobacteriumsp. strain ATCC 27551 andBrevundimonas diminutaMG. Insertional mutation of theopdAgene produced a strain lacking the ability to hydrolyze OPs, suggesting that this is the only gene encoding an OP-hydrolyzing enzyme inA. radiobacterP230. The OPH and OpdA proteins, encoded byopdandopdA, respectively, were overexpressed and purified as maltose-binding proteins, and the maltose-binding protein moiety was cleaved and removed. Neither protein was able to hydrolyze the aliphatic OP malathion. The kinetics of the two proteins for diethyl OPs were comparable. For dimethyl OPs, OpdA had a higherkcatthan OPH. It was also capable of hydrolyzing the dimethyl OPs phosmet and fenthion, which were not hydrolyzed at detectable levels by OPH.
tfdA
-Like Genes in 2,4-Dichlorophenoxyacetic Acid-Degrading Bacteria Belonging to the
Bradyrhizobium-Agromonas-Nitrobacter-Afipia
Cluster in α-
Proteobacteria
Authors: Itoh Kazuhito , Kanda Rie , Sumita Yoko , Kim Hongik , Kamagata Yoichi , Suyama Kousuke , Yamamoto Hiroki , Hausinger Robert P. , Tiedje James M.
Published: July 2002

The 2,4-dichlorophenoxyacetate (2,4-D)/α-ketoglutarate dioxygenase gene (
tfdA
) homolog designated
tfdAα
was cloned and characterized from 2,4-D-degrading bacterial strain RD5-C2. This Japanese upland soil isolate belongs to the
Bradyrhizobium-Agromonas-Nitrobacter-Afipia
cluster in the α subdivision of the class
Proteobacteria
on the basis of its 16S ribosomal DNA sequence. Sequence analysis showed 56 to 60% identity of
tfdAα
to representative
tfdA
genes. A MalE-TfdAα fusion protein expressed in
Escherichia coli
exhibited about 10 times greater activity for phenoxyacetate than 2,4-D in an α-ketoglutarate- and Fe(II)-dependent reaction. The deduced amino acid sequence of TfdAα revealed a conserved His-X-Asp-X
146
-His-X
14
-Arg motif characteristic of the active site of group II α-ketoglutarate-dependent dioxygenases. The
tfdAα
genes were also detected in 2,4-D-degrading α-
Proteobacteria
previously isolated from pristine environments in Hawaii and in Saskatchewan, Canada (Y. Kamagata, R. R. Fulthorpe, K. Tamura, H. Takami, L. J. Forney, and J. M. Tiedje, Appl. Environ. Microbiol.
63:
2266-2272, 1997). These findings indicate that the
tfdA
genes in β- and γ-
Proteobacteria
and the
tfdAα
genes in α-
Proteobacteria
arose by divergent evolution from a common ancestor.
Fitness of
Salmonella enterica
serovar Thompson in the Cilantro Phyllosphere
Authors: Brandl Maria T. , Mandrell Robert E.
Published: July 2002

The epiphytic fitness of
Salmonella enterica
was assessed on cilantro plants by using a strain of
S. enterica
serovar Thompson that was linked to an outbreak resulting from cilantro.
Salmonella
serovar Thompson had the ability to colonize the surface of cilantro leaves, where it was detected by confocal laser scanning microscopy (CLSM) at high densities on the veins and in natural lesions. The population sizes of two common colonizers of plant surfaces,
Pantoea agglomerans
and
Pseudomonas chlororaphis
, were 10-fold higher than that of the human pathogen on cilantro incubated at 22°C. However,
Salmonella
serovar Thompson achieved significantly higher population levels and accounted for a higher proportion of the total culturable bacterial flora on cilantro leaves when the plants were incubated at warm temperatures, such as 30°C, after inoculation, indicating that the higher growth rates exhibited by
Salmonella
serovar Thompson at warm temperatures may increase the competitiveness of this organism in the phyllosphere. The tolerance of
Salmonella
serovar Thompson to dry conditions on plants at 60% relative humidity was at least equal to that of
P. agglomerans
and
P. chlororaphis
. Moreover, after exposure to low humidity on cilantro,
Salmonella
serovar Thompson recovered under high humidity to achieve its maximum population size in the cilantro phyllosphere. Visualization by CLSM of green fluorescent protein-tagged
Salmonella
serovar Thompson and dsRed-tagged
P. agglomerans
inoculated onto cilantro revealed that the human pathogen and the bacterial epiphyte formed large heterogeneous aggregates on the leaf surface. Our studies support the hypothesis that preharvest contamination of crops by
S. enterica
plays a role in outbreaks linked to fresh fruits and vegetables.
Evidence of Association of Salmonellae with Tomato Plants Grown Hydroponically in Inoculated Nutrient Solution
Authors: Guo Xuan , van Iersel Marc W. , Chen Jinru , Brackett Robert E. , Beuchat Larry R.
Published: July 2002

The possibility of uptake of salmonellae by roots of hydroponically grown tomato plants was investigated. Within 1 day of exposure of plant roots to Hoagland nutrient solution containing 4.46 to 4.65 log
10
CFU of salmonellae/ml, the sizes of the pathogen populations were 3.01 CFU/g of hypocotyls and cotyledons and 3.40 log
10
CFU/g of stems for plants with intact root systems (control) and 2.55 log
10
CFU/g of hypocotyls and cotyledons for plants from which portions of the roots had been removed. A population of ≥3.38 log
10
CFU/g of hypocotyls-cotyledons, stems, and leaves of plants grown for 9 days was detected regardless of the root condition. Additional studies need to be done to unequivocally demonstrate that salmonellae can exist as endophytes in tomato plants grown under conditions that simulate commonly used agronomic practices.
Catalase, a Specific Antigen in the Feces of Human Subjects Infected with
Helicobacter pylori
Authors: Suzuki Nobuyuki , Wakasugi Masahiko , Nakaya Seigo , Kokubo Naomi , Sato Masami , Kajiyama Hirofumi , Takahashi Ryoki , Hirata Haruhisa , Ezure Yohji , Fukuda Yoshihiro , Shimoyama Takashi
Published: July 2002

Recently, we reported the production of three new monoclonal antibodies with high specificity for a
Helicobacter pylori
antigen suitable for diagnosis of
H. pylori
infection. The aim of the present study was to identify the antigen recognized by these monoclonal antibodies concerning both
H. pylori
and the feces of human subjects infected with
H. pylori
. The cellular antigen was purified from an
H. pylori
cell extract by immunoaffinity column chromatography with the monoclonal antibody as a ligand. The amino-terminal amino acid sequences (eight residues) of the purified antigen and
H. pylori
catalase were the same. The molecular weights of native and subunit, specific catalase activity, and UV and visible spectra of the purified antigen were in good agreement with those of
H. pylori
catalase. The human fecal antigens were purified from two fecal samples of two
H. pylori
-positive subjects by ammonium sulfate precipitation, CM-Sephadex C
50
chromatography, and the same immunoaffinity chromatography used for the
H. pylori
cellular antigen. The fecal antigens had catalase activity. The amino-terminal amino acid sequences (five residues) of the human fecal antigen and
H. pylori
catalase were the same. The monoclonal antibodies reacted with the native cellular antigen, but did not react with the denatured antigen, human catalase, and bovine catalase. The results show that the target antigen of the monoclonal antibodies is native
H. pylori
catalase and that the monoclonal antibodies are able to specifically detect the antigen, which exists in an intact form, retaining the catalase activity in human feces.
Time Course of Humoral and Cell-Mediated Immune Responses to Human Papillomavirus Type 16 in Infected Women
Authors: Nakagawa Mayumi , Viscidi Raphael , Deshmukh Ian , Costa Maria Da , Palefsky Joel M. , Farhat Sepideh , Moscicki Anna-Barbara
Published: July 2002

The time course of cell-mediated and humoral immune responses was elucidated in eight women with human papillomavirus type 16 (HPV-16) infection by performing serial HPV-16 E6 and E7 cytotoxic T-lymphocyte (CTL) assays and HPV-16 virus-like particle (VLP) antibody analyses. Four subjects had a single incident of HPV-16 DNA detection, and four subjects had two periods of HPV-16 DNA detection. In two of the women in the latter group, the second episode of HPV-16 detection occurred in the presence of high titers of HPV-16 VLP antibody, bringing into question the protective role of humoral immunity in preventing repeated infection. However, all four subjects rapidly became HPV-16 DNA negative following the second detection of HPV-16 DNA, suggesting the presence of immunological memory. In addition, one subject rapidly became negative for HPV-16 DNA despite having no evidence of CTL or VLP antibody response prior to the second HPV-16 DNA detection, suggesting the presence of immunological responses at an undetectable level. Overall, seven of eight subjects (88%) had detectable HPV-16 E6 and/or E7 CTL responses and seven of eight women (88%) had detectable HPV-16 VLP antibody responses.
Ability of the Borreliacidal Antibody Test To Confirm Lyme Disease in Clinical Practice
Authors: Callister Steven M. , Jobe Dean A. , Agger William A. , Schell Ronald F. , Kowalski Todd J. , Lovrich Steven D. , Marks Jennifer A.
Published: July 2002

Highly specific borreliacidal antibodies are induced by infection withBorrelia burgdorferi, and a borreliacidal antibody test (BAT) may be an accurate laboratory procedure for confirming Lyme disease in clinical practice. To investigate this, 34 Lyme disease sera and 34 sera from patients with other illnesses who had presented to a primary-care facility located in an area of borreliosis endemicity were tested by the BAT and Western blotting (WB). The BAT was more sensitive (79% versus 65%;P= 0.090), especially in cases in which patients had a single erythema migrans lesion (P= 0.021). In addition, the potentially cross-reactive sera were negative by the BAT but WB yielded three (9%) false-positive results. The results from 104 sera from possible Lyme disease patients demonstrated the clinical usefulness of the more sensitive and specific BAT. The BAT was positive for 40 (38%) sera from patients with Lyme disease-related symptoms and appropriate clinical and epidemiological findings. WB confirmed Lyme disease in 30 (75%) of the 40 BAT-positive patients but failed to detectB. burgdorferiinfection in 10 BAT-positive patients. WB was also positive for 11 BAT-negative sera, but six (55%) patients had case histories which suggested that the results were false positives. Collectively, the results confirm that the BAT is a sensitive and highly specific test and suggest that widespread use would increase the accuracy of serodiagnostic confirmation of Lyme disease.
Influence of Antimalarial Treatment on Acquisition of Immunity in
Plasmodium berghei
NK65 Malaria
Authors: Long Ton That Ai , Nakazawa Shusuke , Huaman Maria Cecilia , Kanbara Hiroji
Published: July 2002

Antimalarial treatments during primary
Plasmodium berghei
NK65 infection in BALB/c mice influenced the acquisition of protective immunity against reinfection. Among subcurative treatments, lower doses better enable mice to acquire protective immunity than do higher doses. Eradication of parasites from the start of infection did not promote protective immunity.
Interleukin-8 and Tumor Necrosis Factor Alpha Production in Human Epidermal Keratinocytes Induced byTrichophyton mentagrophytes
Authors: Nakamura Yuka , Kano Rui , Hasegawa Atsuhiko , Watanabe Shinichi
Published: July 2002

Production of interleukin-8 (IL-8) and tumor necrosis factor alpha (TNF-α) was confirmed by enzyme-linked immunosorbent assay in a medium where human epidermal keratinocytes were cocultured withTrichophyton mentagrophytesfor 1 to 12 h. IL-8 and TNF-α mRNAs were also detected in the keratinocytes cocultured withT. mentagrophytes.
Immunization with the Recombinant PorB Outer Membrane Protein Induces a Bactericidal Immune Response against
Neisseria meningitidis
Authors: Wright J. Claire , Williams Jeannette N. , Christodoulides Myron , Heckels John E.
Published: July 2002

Infections with
Neisseria meningitidis
are characterized by life-threatening meningitis and septicemia. The meningococcal porin proteins from serogroup B meningococci have been identified as candidates for inclusion in vaccines to prevent such infections. In this study, we investigated the vaccine potential of the PorB porin protein free of other meningococcal components. The
porB
gene from a strain of
Neisseria meningitidis
expressing the class 3 outer membrane porin protein (PorB3) was cloned into the pRSETB vector, and the protein was expressed at high levels in a heterologous host
Escherichia coli
. The recombinant protein was purified to homogeneity by affinity chromatography and used for immunization after incorporation into liposomes and into micelles composed either of zwitterionic detergent or nondetergent sulfobetaine. The immunogenicity of these preparations was compared to recombinant PorB protein adsorbed to Al(OH)
3
adjuvant as a control. Although sera raised against the protein adsorbed to Al(OH)
3
reacted with the purified recombinant protein, sera raised against liposomes and micelles showed greater activity with native protein, as measured by enzyme immunoassay with outer membranes and by whole-cell immunofluorescence. Reactivity with native protein was considerably enhanced by incorporation of the adjuvant monophosphoryl lipid A into the liposome or micelle preparations. Recognition of the native protein was in a serotype-specific manner and was associated with the ability of the antisera to promote high levels of serotype-specific complement-mediated killing of meningococci. These results demonstrate that the PorB protein should be considered as a component of a vaccine designed to prevent serogroup B meningococcal infection.
Interaction ofNeisseria meningitidiswith Human Meningeal Cells Induces the Secretion of a Distinct Group of Chemotactic, Proinflammatory, and Growth-Factor Cytokines
Authors: Christodoulides Myron , Makepeace Benjamin L. , Partridge Kris A. , Kaur Davindaur , Fowler Mark I. , Weller Roy O. , Heckels John E.
Published: July 2002

The interactions ofNeisseria meningitidiswith cells of the leptomeninges are pivotal events in the progression of bacterial leptomeningitis. An in vitro model based on the culture of human meningioma cells was used to investigate the role of the leptomeninges in the inflammatory response. Following challenge with meningococci, meningioma cells secreted specifically the proinflammatory cytokine interleukin-6 (IL-6), the CXC chemokine IL-8, the CC chemokines monocyte chemoattractant protein 1 (MCP-1) and regulated-upon-activation, normal-T-cell expressed and secreted protein (RANTES), and the cytokine growth factor granulocyte-macrophage colony-stimulating factor (GM-CSF). A temporal pattern of cytokine production was observed, with early secretion of IL-6, IL-8, and MCP-1 followed by later increases in RANTES and GM-CSF levels. IL-6 was induced equally by the interactions of piliated and nonpiliated meningococci, whereas lipopolysaccharide (LPS) had a minimal effect, suggesting that other, possibly secreted, bacterial components were responsible. Induction of IL-8 and MCP-1 also did not require adherence of bacteria to meningeal cells, but LPS was implicated. In contrast, efficient stimulation of RANTES by intact meningococci required pilus-mediated adherence, which served to deliver increased local concentrations of LPS onto the surface of meningeal cells. Secretion of GM-CSF was induced by pilus-mediated interactions but did not involve LPS. In addition, capsule expression had a specific inhibitory effect on GM-CSF secretion, which was not observed with IL-6, IL-8, MCP-1, or RANTES. Thus, the data demonstrate that cells of the leptomeninges are not inert but are active participants in the innate host response during leptomeningitis and that there is a complex relationship between expression of meningococcal components and cytokine induction.
Lipopolysaccharide-Binding Protein- and CD14-Dependent Activation of Mitogen-Activated Protein Kinase p38 by Lipopolysaccharide in Human Neutrophils Is Associated with Priming of Respiratory Burst
Authors: Yan Sen Rong , Al-Hertani Walla , Byers David , Bortolussi Robert
Published: July 2002

Neutrophil (PMN) functions can be primed for greatly increased oxidative radical release by exposure to certain agents such as lipopolysaccharide (LPS). Although a variety of signaling pathways involving both tyrosine kinases and mitogen-activated protein (MAP) kinases may be operative, the mechanisms of PMN priming are still not understood. We found that PMN priming was not achieved by treatment of cells with a very low concentration (5 ng/ml) of LPS unless additional “helper” factors were present in plasma (5%). Under these conditions, LPS induced tyrosine phosphorylation of a 38-kDa protein, which was coincident with the MAP kinase p38 action in this situation. LPS-mediated activation of p38 in human PMNs was dependent on the presence of LPS binding protein from plasma and CD14 on the surfaces of the cells. Phosphorylation of p38 was highly correlated with LPS priming of a formyl-methionyl-leucyl-phenylalanine (fMLP)-stimulated PMN respiratory burst. Treatment of PMN with the p38-specific inhibitor SB203580 significantly attenuated the respiratory burst in cells primed by LPS and stimulated by fMLP. These results suggest that the LPS signaling pathway leading to p38 activation may be an important mechanism in regulation of PMN priming. The mediator(s) linking CD14 to p38 involves proteins that are functionally sensitive to genistein but insensitive to tyrphostin AG126 and to Src- and Syk-family kinase, protein kinase C, and phosphatidylinositol 3-kinase inhibitors. Elucidating this pathway will provide insight into possible regulation of PMN priming by LPS.