bluuebunny/crossref_metadata_2025 huggingface dataset:
Experiments and Simulations of Ion-Enhanced Interfacial Chemistry on Aqueous NaCl Aerosols
Authors: Knipping E. M. , Lakin M. J. , Foster K. L. , Jungwirth P. , Tobias D. J. , Gerber R. B. , Dabdub D. , Finlayson-Pitts B. J.
Published: July 2002

A combination of experimental, molecular dynamics, and kinetics modeling studies is applied to a system of concentrated aqueous sodium chloride particles suspended in air at room temperature with ozone, irradiated at 254 nanometers to generate hydroxyl radicals. Measurements of the observed gaseous molecular chlorine product are explainable only if reactions at the air-water interface are dominant. Molecular dynamics simulations show the availability of substantial amounts of chloride ions for reaction at the interface, and quantum chemical calculations predict that in the gas phase chloride ions will strongly attract hydroxl radicals. Model extrapolation to the marine boundary layer yields daytime chlorine atom concentrations that are in good agreement with estimates based on field measurements of the decay of selected organics over the Southern Ocean and the North Atlantic. Thus, ion-enhanced interactions with gases at aqueous interfaces may play a more generalized and important role in the chemistry of concentrated inorganic salt solutions than was previously recognized.
Language Discrimination by Human Newborns and by Cotton-Top Tamarin Monkeys
Authors: Ramus Franck , Hauser Marc D. , Miller Cory , Morris Dylan , Mehler Jacques
Published: July 2002

Humans, but no other animal, make meaningful use of spoken language. What is unclear, however, is whether this capacity depends on a unique constellation of perceptual and neurobiological mechanisms or whether a subset of such mechanisms is shared with other organisms. To explore this problem, parallel experiments were conducted on human newborns and cotton-top tamarin monkeys to assess their ability to discriminate unfamiliar languages. A habituation-dishabituation procedure was used to show that human newborns and tamarins can discriminate sentences from Dutch and Japanese but not if the sentences are played backward. Moreover, the cues for discrimination are not present in backward speech. This suggests that the human newborns' tuning to certain properties of speech relies on general processes of the primate auditory system.
Evidence for Brainstem Structures Participating in Oculomotor Integration
Authors: Nakamagoe K. , Iwamoto Y. , Yoshida K.
Published: July 2002

The cerebellar flocculus has been implicated in vestibulo-oculomotor control. One major central input to this structure originates from brainstem cells in the paramedian tract (PMT), whose function is unknown. Here it is reported that PMT cells in the pons carry vestibular and eye movement signals and their pharmacological inactivation produces a leaky integrator combined with vestibular imbalance. The results suggest that PMT cells provide the cerebellum with sensory and motor signals that are essential for velocity-to-position integration, a common premotor process that is required in all motor systems.
Rapid Destruction of Human Cdc25A in Response to DNA Damage
Authors: Mailand Niels , Falck Jacob , Lukas Claudia , Syljuåsen Randi G. , Welcker Markus , Bartek Jiri , Lukas Jiri
Published: July 2002

To protect genome integrity and ensure survival, eukaryotic cells exposed to genotoxic stress cease proliferating to provide time for DNA repair. Human cells responded to ultraviolet light or ionizing radiation by rapid, ubiquitin- and proteasome-dependent protein degradation of Cdc25A, a phosphatase that is required for progression from G
1
to S phase of the cell cycle. This response involved activated Chk1 protein kinase but not the p53 pathway, and the persisting inhibitory tyrosine phosphorylation of Cdk2 blocked entry into S phase and DNA replication. Overexpression of Cdc25A bypassed this mechanism, leading to enhanced DNA damage and decreased cell survival. These results identify specific degradation of Cdc25A as part of the DNA damage checkpoint mechanism and suggest how Cdc25A overexpression in human cancers might contribute to tumorigenesis.
Interconnected Feedback Loops in the
Neurospora
Circadian System
Authors: Lee Kwangwon , Loros Jennifer J. , Dunlap Jay C.
Published: July 2002

In
Neurospora crassa
, white collar 1 (WC-1), a transcriptional activator and positive clock element, is rhythmically expressed from a nonrhythmic steady-state pool of
wc-1
transcript, consistent with posttranscriptional regulation of rhythmicity. Mutations in
frq
influence both the level and periodicity of WC-1 expression, and driven FRQ expression not only depresses its own endogenous levels, but positively regulates WC-1 synthesis with a lag of about 8 hours, a delay similar to that seen in the wild-type clock. FRQ thus plays dual roles in the
Neurospora
clock and thereby, with WC-1, forms a second feedback loop that would promote robustness and stability in this circadian system. The existence also of interlocked loops in
Drosophila melanogaster
and mouse clocks suggests that such interlocked loops may be a conserved aspect of circadian timing systems.
An Empirical Assessment of Taxic Paleobiology
Authors: Adrain Jonathan M. , Westrop and Stephen R.
Published: July 2002

The analysis of major changes in faunal diversity through time is a central theme of analytical paleobiology. The most important sources of data are literature-based compilations of stratigraphic ranges of fossil taxa. The levels of error in these compilations and the possible effects of such error have often been discussed but never directly assessed. We compared our comprehensive database of trilobites to the equivalent portion of J. J. Sepkoski Jr.'s widely used global genus database. More than 70% of entries in the global database are inaccurate; however, as predicted, the error is randomly distributed and does not introduce bias.
Central Role for the Lens in Cave Fish Eye Degeneration
Authors: Yamamoto Yoshiyuki , Jeffery William R.
Published: July 2002

Astyanax mexicanus
is a teleost with eyed surface-dwelling and eyeless cave-dwelling forms. Eye formation is initiated in cave fish embryos, but the eye subsequently arrests and degenerates. The surface fish lens stimulates growth and development after transplantation into the cave fish optic cup, restoring optic tissues lost during cave fish evolution. Conversely, eye growth and development are retarded following transplantation of a surface fish lens into a cave fish optic cup or lens extirpation. These results show that evolutionary changes in an inductive signal from the lens are involved in cave fish eye degeneration.
Unmasking Electronic Energy Transfer of Conjugated Polymers by Suppression of O
2
Quenching
Authors: Yu Ji , Hu Dehong , Barbara Paul F.
Published: July 2002

The photochemistry of poly[2-methoxy, 5-(2′-ethyl-hexyloxy)-
p
-phenylene-vinylene] (MEH-PPV) has been found to be highly dependent on the presence of O
2
, which increases singlet exciton quenching dramatically. Spectroscopy on isolated single molecules of MEH-PPV in polycarbonate films that exclude O
2
reveals two distinct polymer conformations with fluorescence maxima near 555 and 580 nanometers wavelength, respectively. Time-resolved single-molecule data demonstrate that the 580-nanometer conformation exhibits a “landscape” for intramolecular electronic energy relaxation with a “funnel” that contains a 580-nanometer singlet exciton trap at the bottom. The exciton traps can be converted to exciton quenchers by reaction with O
2
. Conformationally induced, directed-energy transfer is arguably a critical dynamical process that is responsible for many of the distinctive photophysical properties of conjugated polymers.
Topologically Linked Protein Rings in the Bacteriophage HK97 Capsid
Authors: Wikoff William R. , Liljas Lars , Duda Robert L. , Tsuruta Hiro , Hendrix Roger W. , Johnson John E.
Published: July 2002

The crystal structure of the double-stranded DNA bacteriophage HK97 mature empty capsid was determined at 3.6 angstrom resolution. The 660 angstrom diameter icosahedral particle contains 420 subunits with a new fold. The final capsid maturation step is an autocatalytic reaction that creates 420 isopeptide bonds between proteins. Each subunit is joined to two of its neighbors by ligation of the side-chain lysine 169 to asparagine 356. This generates 12 pentameric and 60 hexameric rings of covalently joined subunits that loop through each other, creating protein chainmail: topologically linked protein catenanes arranged with icosahedral symmetry. Catenanes have not been previously observed in proteins and provide a stabilization mechanism for the very thin HK97 capsid.
Diversity and Dynamics of Dendritic Signaling
Authors: Häusser Michael , Spruston Nelson , Stuart Greg J.
Published: July 2002

Communication between neurons in the brain occurs primarily through synapses made onto elaborate treelike structures called dendrites. New electrical and optical recording techniques have led to tremendous advances in our understanding of how dendrites contribute to neuronal computation in the mammalian brain. The varied morphology and electrical and chemical properties of dendrites enable a spectrum of local and long-range signaling, defining the input-output relationship of neurons and the rules for induction of synaptic plasticity. In this way, diversity in dendritic signaling allows individual neurons to carry out specialized functions within their respective networks.
Solar Wind Record on the Moon: Deciphering Presolar from Planetary Nitrogen
Authors: Hashizume Ko , Chaussidon Marc , Marty Bernard , Robert François
Published: July 2002

Ion microprobe analyses show that solar wind nitrogen associated with solar wind hydrogen implanted in the first tens of nanometers of lunar regolith grains is depleted in
15
N by at least 24% relative to terrestrial atmosphere, whereas a nonsolar component associated with deuterium-rich hydrogen, detected in silicon-bearing coatings at the surface of some ilmenite grains, is enriched in
15
N. Systematic enrichment of
15
N in terrestrial planets and bulk meteorites relative to the protosolar gas cannot be explained by isotopic fractionation in nebular or planetary environments but requires the contribution of
15
N-rich compounds to the total nitrogen in planetary materials. Most of these compounds are possibly of an interstellar origin and never equilibrated with the
15
N-depleted protosolar nebula.
Chromosomal Effects of Rapid Gene Evolution in
Drosophila melanogaster
Authors: Nurminsky Dmitry , Aguiar Daniel De , Bustamante Carlos D. , Hartl Daniel L.
Published: July 2002

Rapid adaptive fixation of a new favorable mutation is expected to affect neighboring genes along the chromosome. Evolutionary theory predicts that the chromosomal region would show a reduced level of genetic variation and an excess of rare alleles. We have confirmed these predictions in a region of the X chromosome of
Drosophila melanogaster
that contains a newly evolved gene for a component of the sperm axoneme. In
D. simulans
, where the novel gene does not exist, the pattern of genetic variation is consistent with selection against recurrent deleterious mutations. These findings imply that the pattern of genetic variation along a chromosome may be useful for inferring its evolutionary history and for revealing regions in which recent adaptive fixations have taken place.
Dynamic Optimization of Odor Representations by Slow Temporal Patterning of Mitral Cell Activity
Authors: Friedrich Rainer W. , Laurent Gilles
Published: July 2002

Mitral cells (MCs) in the olfactory bulb (OB) respond to odors with slow temporal firing patterns. The representation of each odor by activity patterns across the MC population thus changes continuously throughout a stimulus, in an odor-specific manner. In the zebrafish OB, we found that this distributed temporal patterning progressively reduced the similarity between ensemble representations of related odors, thereby making each odor's representation more specific over time. The tuning of individual MCs was not sharpened during this process. Hence, the individual responses of MCs did not become more specific, but the odor-coding MC assemblies changed such that their overlap decreased. This optimization of ensemble representations did not occur among olfactory afferents but resulted from OB circuit dynamics. Time can therefore gradually optimize stimulus representations in a sensory network.
Inhibition of Cyclin-Dependent Kinase Activity and Induction of Apoptosis by Preussin in Human Tumor Cells
Authors: Achenbach Tatjana V. , Slater Emily P. , Brummerhop Harm , Bach Thorsten , Müller Rolf
Published: July 2002

In this paper, we report that (+)-preussin, a pyrrolidinol alkaloid originally identified as an antifungal agent, has growth-inhibitory and cytotoxic effects on human cancer cells. Preussin was found to be a potent inhibitor of cyclin E kinase (CDK2-cyclin E) in vitro (50% inhibitory concentration; ∼500 nM) and to inhibit cell cycle progression into S phase. In agreement with these findings, the level of the cyclin-dependent kinase inhibitor p27KIP-1is increased in response to preussin treatment while the expression of both cyclin A and the transcription factor E2F-1 is down-regulated. Preussin also induces programmed cell death (apoptosis), which requires caspase activation and involves the release of cytochromecfrom mitochondria. This induction of apoptosis is not blocked by high levels of Bcl-2, which usually confers resistance to chemotherapeutic agents. Taken together, our data indicate that preussin could be a promising lead compound for the development of a new class of potent antitumor drugs.
Regional Prophylaxis with Teicoplanin in Monolateral or Bilateral Total Knee Replacement: an Open Study
Authors: de Lalla Fausto , Viola Renato , Pellizzer Giampietro , Lazzarini Luca , Tramarin Andrea , Fabris Paolo
Published: July 2002

From January 1991 to June 1997, patients undergoing primary elective monolateral or bilateral total knee replacement (TKR) were consecutively enrolled in a prospective, open clinical study on the efficacy and safety of regional prophylaxis with teicoplanin (TEC). Those scheduled for monolateral TKR (115 patients) received 400 mg of TEC in 100 ml of saline as a 5-min infusion into a foot vein of the leg to be operated on immediately after the tourniquet was inflated to 400 mm Hg (ca. 50 kPa). For patients undergoing bilateral surgery (45 patients), regional administration of TEC was also repeated for the second knee operation. Follow-up ranged from a minimum of 2 years to 8 years. None of the patients experienced local or systemic adverse effects following regional administration of TEC. In the immediate postoperative and 2-year follow-up periods, only one superficial infection of the primary site attributable to intraoperative contamination (prophylaxis failure) out of the 205 prostheses implanted was observed. Deep infections involving the prosthesis did not occur. Infectious complications at distant sites were observed in nine cases (urinary tract infection due to
Escherichia coli
in eight cases, and
Salmonella enteritidis
gastroenteritis in one case) in the immediate postoperative period; they all were rapidly cured after antibiotic treatment. A delayed prosthetic infection, related to hematogenous spread of the etiological agent and therefore not considered a prophylactic failure, was observed in a patient who had undergone TKR 5 years before. Regional administration of TEC in monolateral and bilateral TKR appears to be a safe and valuable prophylactic technique.
Antibiotic Resistance in the ECOR Collection: Integrons and Identification of a Novel
aad
Gene
Authors: Mazel Didier , Dychinco Broderick , Webb Vera A. , Davies Julian
Published: July 2002

The 72
Escherichia coli
strains of the ECOR collection were examined for resistance to 10 different antimicrobial agents including ampicillin, tetracycline, mercury, trimethoprim, and sulfonamides. Eighteen strains were resistant to at least one of the antibiotics tested, and nearly 20% (14 of 72) were resistant to two or more. Several of the resistance determinants were shown to be carried on conjugative elements. The collection was screened for the presence of the three classes of integrons and for the
sul1
gene, which is generally associated with class 1 integrons. The four strains found to carry a class 1 integron also had Tn
21
-encoded mercury resistance. One of the integrons encoded a novel streptomycin resistance gene,
aadA7
, with an
attC
site (or 59-base element) nearly identical to the
attC
site associated with the
qacF
gene cassette found in In40 (M.-C. Ploy, P. Courvalin, and T. Lambert, Antimicrob. Agents Chemother. 42:2557–2563, 1998). The conservation of associated
attC
sites among unrelated resistance cassettes is similar to arrangements found in the
Vibrio cholerae
superintegrons (D. Mazel, B. Dychinco, V. A. Webb, and J. Davies, Science 280:605–608, 1998) and supports the hypothesis that resistance cassettes are picked up from superintegron pools and independently assembled from unrelated genes and related
attC
sites.
Unusual Susceptibility of a Multidrug-Resistant Yeast Strain to Peptidic Antifungals
Authors: Milewski Sławomir , Mignini Fiorenzo , Prasad Rajendra , Borowski Edward
Published: July 2002

The susceptibility of
Saccharomyces cerevisiae
JG436 multidrug transporter deletion mutant, Δ
pdr5
, to several antifungal agents was compared to that of JG436-derived JGCDR1 and JGCaMDR1 transformants, harboring the
CDR1
and
CaMDR1
genes, encoding the main drug-extruding membrane proteins of
Candida albicans
. The JGCDR1 and JGCaMDR1 yeasts demonstrated markedly diminished susceptibility to the azole antifungals, terbinafine and cycloheximide, while that to amphotericin B was unchanged. Surprisingly, JGCDR1 but not JGCaMDR1 cells showed enhanced susceptibility to peptidic antifungals, rationally designed compounds containing inhibitors of glucosamine-6-phosphate synthase. It was found that these antifungal oligopeptides, as well as model oligopeptides built of proteinogenic amino acids, were not effluxed from JGCDR1 cells. Moreover, they were taken up by these cells at rates two to three times higher than by JG436. The tested oligopeptides were rapidly cleaved to constitutive amino acids by cytoplasmic peptidases. Studies on the mechanism of the observed phenomenon suggested that an additive proton motive force generated by Cdr1p stimulated uptake of oligopeptides into JGCDR1 cells, thus giving rise to the higher antifungal activity of FMDP [
N
3
-(4-methoxyfumaroyl)-
l
-2,3-diaminopropanoic acid]-peptides.
Pharmacokinetics of Stavudine and Didanosine Coadministered with Nelfinavir in Human Immunodeficiency Virus-Exposed Neonates
Authors: Rongkavilit Chokechai , Thaithumyanon Pimolrat , Chuenyam Theshinee , Damle Bharat D. , Limpongsanurak Sompop , Boonrod Chantana , Srigritsanapol Aeumporn , Hassink Elly A. M. , Hoetelmans Richard M. W. , Cooper David A. , Lange Joep M. A. , Ruxrungtham Kiat , Phanuphak Praphan
Published: July 2002

We evaluated the pharmacokinetics of stavudine (d4T) and didanosine (ddI) in neonates. Eight neonates born to human immunodeficiency virus-infected mothers were enrolled to receive 1 mg of d4T per kg of body weight twice daily and 100 mg of ddI per m
2
once daily in combination with nelfinavir for 4 weeks after birth. Pharmacokinetic evaluations were performed at 14 and 28 days of age. For d4T, on days 14 and 28, the median areas under the concentration-time curves from 0 to 12 h (AUC
0–12
s) were 1,866 and 1,603, ng · h/ml, respectively, and the median peak concentrations (
C
max
s) were 463 and 507 ng/ml, respectively. For ddI, on days 14 and 28, the median AUC
0–10
s were 1,573 and 1,562 h · ng/ml, respectively, and the median
C
max
s were 627 and 687 ng/ml, respectively. Systemic levels of exposure to d4T were comparable to those seen in children, suggesting that the pediatric dose of 1 mg/kg twice daily is appropriate for neonates at 2 to 4 weeks of age. Levels of exposure to ddI were modestly higher than those seen in children. Whether this observation warrants a reduction of the ddI dose in neonates is unclear.
Nonculture Prediction of
Neisseria meningitidis
Susceptibility to Penicillin
Authors: Antignac Aude , Alonso Jean-Michel , Taha Muhamed-Kheir
Published: July 2002

We developed a nonculture method to predict the susceptibility of
Neisseria meningitidis
to penicillin G. The
penA
gene was amplified and submitted to restriction fragment length polymorphism analysis. This approach was first validated with a collection of 75 meningococcal strains of known phenotypes. It was next successfully applied to 29 clinical samples.
Apoptosis Contributes to Amphotericin B- Induced Nephrotoxicity
Authors: Varlam Despina E. , Siddiq Mustafa M. , Parton Lance A. , Rüssmann Holger
Published: July 2002

The aim of this study was to investigate whether apoptosis contributes to nephrotoxicity caused by amphotericin B (AmB). By detecting apoptosis-specific DNA fragmentation, it is demonstrated that proximal tubular cells (LLC-PK
1
) and medullary interstitial cells (RMIC) respond with programmed cell death when treated with therapeutic doses of AmB. Concomitant application of AmB and recombinant human insulin-like growth factor-1 (rhIGF-1), a known antiapoptotic agent, abrogated apoptosis in vitro. To validate that the observed apoptotic effects on renal tissue culture cells are applicable to an in vivo setting, an animal model was used for verification. Therefore, Sprague-Dawley rats were treated with AmB. The drug caused hypokalemia, decreased weight gain, loss of renal concentrating ability, and dehydration in a dose-dependent fashion. Microscopic examination of renal tissue sections revealed apoptotic alterations predominantly in proximal and distal tubular epithelial cells. To verify that the observed clinical side effects were linked to apoptosis, rhIGF-1 was applied concomitantly with AmB. In all animals, rhIGF-1 prevented the above-mentioned clinical side effects. Moreover, significantly reduced apoptosis was observed in renal tissue sections of these animals, indicating the relevance of apoptosis in nephrotoxicity. This is the first report to demonstrate that AmB induces apoptosis in the rat kidney in a dose-dependent fashion. The incidence of apoptosis correlates with renal toxicity and can be abrogated by concomitant treatment with rhIGF-1.
Prolonged Antimicrobial Activity of a Catheter Containing Chlorhexidine-Silver Sulfadiazine Extends Protection against Catheter Infections In Vivo
Authors: Bassetti Stefano , Hu Jean , D'Agostino Ralph B. , Sherertz Robert J.
Published: July 2002

The present study evaluated in vitro and in vivo a new chlorhexidine (C)-silver sulfadiazine (S) vascular catheter (the CS2 catheter) characterized by a higher C content and by the extended release of the surface-bound antimicrobials. The CS2 catheter was compared with a first-generation, commercially available CS catheter (the CS1 catheter). The CS2 catheter produced slightly smaller zones of inhibition (mean difference, 0.9 mm [
P
< 0.001]) at 24 h against
Staphylococcus aureus
and five other microorganisms by several different methodologies. However, in a rabbit model, both CS catheters were similarly efficacious in preventing a catheter infection when the rabbits were inoculated with 10
4
to 10
7
CFU of
S. aureus
at the time of catheter insertion. The CS2 catheter retained its antimicrobial activity significantly longer in vitro and in vivo (half-lifes exceeded 34 and 7 days, respectively) and was also significantly more efficacious in preventing a catheter infection when 10
6
CFU of
S. aureus
was inoculated 2 days after catheter implantation (
P
< 0.001). These results suggest that prolonged anti-infective activity on the external catheter surface provides improved efficacy in the prevention of infection.
Effect of Abolishment of the Use of Antimicrobial Agents for Growth Promotion on Occurrence of Antimicrobial Resistance in Fecal Enterococci from Food Animals in Denmark
Authors: Aarestrup Frank Møller , Seyfarth Anne Mette , Emborg Hanne-Dorthe , Pedersen Karl , Hendriksen René S. , Bager Flemming
Published: July 2002

From 1995 to 2000, a total of 673
Enterococcus faecium
and 1,088
Enterococcus faecalis
isolates from pigs together with 856
E. faecium
isolates from broilers were isolated and tested for susceptibility to four classes of antimicrobial agents used for growth promotion as part of the Danish program of monitoring for antimicrobial resistance. The four antimicrobials were avilamycin, erythromycin, vancomycin, and virginiamycin. Major changes in the use of antimicrobial agents for growth promotion have occurred during the last 6 years in Denmark. The government banned the use of avoparcin in 1995 and of virginiamycin in 1998. Furthermore, the producers have voluntarily stopped all use beginning in 1999. The avoparcin ban in 1995 was followed by a decrease in the occurrence of glycopeptide-resistant
E. faecium
(GRE) in broilers, from 72.7% in 1995 to 5.8% in 2000. The occurrence of glycopeptide resistance among isolates from pigs remained constant at around 20% from 1995 to 1997. It was shown that, in GRE from pigs, the genes encoding macrolide and glycopeptide resistance were genetically linked and that, following the decrease in the use of tylosin during 1998 and 1999, the occurrence of GRE in pigs decreased to 6.0% in 2000. From 1995 to 1997 the occurrence of erythromycin resistance among
E. faecium
and
E. faecalis
isolates from pigs was almost 90%. Use of tylosin decreased considerably during 1998 and 1999, and this decrease was followed by decreases in the occurrence of resistance to 46.7 and 28.1% among
E. faecium
and
E. faecalis
isolates from pigs, respectively. Erythromycin resistance among
E. faecium
isolates from broilers reached a maximum of 76.3% in 1997 but decreased to 12.7% in 2000 concomitantly with more limited use of virginiamycin. Use of virginiamycin increased from 1995 to 1997 and was followed by an increased occurrence of virginiamycin resistance among
E. faecium
isolates in broilers, from 27.3% in 1995 to 66.2% in 1997. In January 1998 the use of virginiamycin was banned in Denmark, and the occurrence of virginiamycin resistance decreased to 33.9% in 2000. Use of avilamycin increased from 1995 to 1996 and was followed by an increase in avilamycin resistance among
E. faecium
isolates from broilers, from 63.6% in 1995 to 77.4% in 1996. Since 1996 avilamycin usage has decreased, followed by a decrease in resistance to 4.8% in 2000. Our observations show that it is possible to reduce the occurrence of antimicrobial resistance in a national population of food animals when the selective pressure is removed. Cases in which resistance to vancomycin was linked to resistance to erythromycin were exceptions. In such cases resistance did not decrease until the use of both avoparcin and tylosin was limited.
Virtual Screening of Combinatorial Libraries across a Gene Family: in Search of Inhibitors of
Giardia lamblia
Guanine Phosphoribosyltransferase
Authors: Aronov Alex M. , Munagala Narsimha R. , Kuntz Irwin D. , Wang Ching C.
Published: July 2002

Parasitic protozoa lack the ability to synthesize purine nucleotides de novo, relying instead on purine salvage enzymes for their survival. Guanine phosphoribosyltransferase (GPRT) from the protozoan parasite
Giardia lamblia
is a potential target for rational antiparasitic drug design, based on the experimental evidence, which indicates the lack of interconversion between adenine and guanine nucleotide pools. The present study is a continuation of our efforts to use three-dimensional structures of parasitic phosphoribosyltransferases (PRTs) to design novel antiparasitic agents. Two micromolar phthalimide-based GPRT inhibitors were identified by screening the in-house phthalimide library. A combination of structure-based scaffold selection using virtual library screening across the PRT gene family and solid phase library synthesis led to identification of smaller (molecular weight, <300) ligands with moderate to low specificity for GPRT; the best inhibitors, GP3 and GP5, had
K

i

values in the 23 to 25 μM range. These results represent significant progress toward the goal of designing potent inhibitors of purine salvage in
Giardia
parasites. As a second step in this process, altering the phthalimide moiety to optimize interactions in the guanine-binding pocket of GPRT is expected to lead to compounds with promising activity against
G. lamblia
PRT.
Gatifloxacin Efficacy in Treatment of Experimental Methicillin-Sensitive
Staphylococcus aureus
-Induced Osteomyelitis in Rabbits
Authors: Shirtliff Mark E. , Calhoun Jason H. , Mader Jon T.
Published: July 2002

The effectiveness of oral gatifloxacin was compared to that of standard parenteral antibiotic therapy (nafcillin) for the treatment of experimental methicillin-sensitive
Staphylococcus aureus
-induced osteomyelitis in a rabbit model. Gatifloxacin was as effective as nafcillin in clearing the infection. Therefore, oral gatifloxacin treatment of osteomyelitis may be an effective alternative to intravenous nafcillin treatment.
Efficacy of Minocycline and EDTA Lock Solution in Preventing Catheter-Related Bacteremia, Septic Phlebitis, and Endocarditis in Rabbits
Authors: Raad Issam , Hachem Ray , Tcholakian Robert K. , Sherertz Robert
Published: July 2002

To determine the efficacy of antibiotic catheter lock solution in preventing catheter-related infections, silicone catheters were tunneled and inserted into the jugular veins of 18 rabbits. The catheters were challenged with an intraluminal injection of 10
5
CFU of slime-producing
Staphylococcus epidermidis
in 0.1 ml of water. The catheters were maintained on heparin (100 IU/ml) flush for the first 3 days. On day 3, quantitative blood samples for culture were obtained from the catheters and ear veins, which documented catheter-related bacteremia, and the rabbits were randomized to have their catheters flushed as follows: five animals were continued on heparin (100 IU/ml), five animals received vancomycin (3 mg/ml) with heparin (100 IU/ml), and eight animals received 3 mg of minocycline per ml with 30 mg of EDTA per ml (M-EDTA). All animals were killed at day 7. Blood, catheters, jugular veins, and heart valves were cultured quantitatively. Animals maintained on heparin developed catheter-related colonization, bacteremia, septic phlebitis, and endocarditis. Vancomycin-heparin partially prevented catheter colonization, bacteremia, and phlebitis (
P
= 0.2). M-EDTA completely prevented catheter colonization, catheter-related bacteremia, and phlebitis in all of the animals (
P
< 0.01). Tricuspid endocarditis was equally prevented by vancomycin-heparin and M-EDTA (
P
≤ 0.06). In conclusion, the M-EDTA catheter flush solution was highly efficacious in preventing catheter-related colonization, bacteremia, septic phlebitis, and endocarditis in rabbits.
Impact of Trimethoprim-Sulfamethoxazole Prophylaxis on Etiology and Susceptibilities of Pathogens Causing Human Immunodeficiency Virus-Associated Bacteremia
Authors: Wininger David A. , Fass Robert J.
Published: July 2002

The impact of chronic prophylactic administration of trimethoprim-sulfamethoxazole (SXT) on the ecology and the antimicrobial susceptibilities of bloodstream pathogens in human immunodeficiency virus (HIV)-infected patients was studied using a retrospective chart review. Eighty-nine patients with advanced HIV infection developed 124 episodes of bacteremia with 156 pathogenic isolates.
Staphylococcus aureus
and
Enterobacteriaceae
tended to be less common among patients receiving SXT. Isolates from patients receiving SXT were likelier (75%) to be resistant to 20 μg of SXT/ml than those from patients not receiving SXT (33%) (
P
< 0.001).
Involvement of an Extracellular Protease in Algicidal Activity of the Marine Bacterium
Pseudoalteromonas
sp. Strain A28
Authors: Lee Sun-og , Kato Junichi , Takiguchi Noboru , Kuroda Akio , Ikeda Tsukasa , Mitsutani Atsushi , Ohtake Hisao
Published: July 2002

The marine bacterium
Pseudoalteromonas
sp. strain A28 was able to kill the diatom
Skeletonema costatum
strain NIES-324. The culture supernatant of strain A28 showed potent algicidal activity when it was applied to a paper disk placed on a lawn of
S. costatum
NIES-324. The condensed supernatant, which was prepared by subjecting the A28 culture supernatant to ultrafiltration with a 10,000-
M
w
-cutoff membrane, showed algicidal activity, suggesting that strain A28 produced extracellular substances capable of killing
S. costatum
cells. The condensed supernatant was then found to have protease and DNase activities. Two
Pseudoalteromonas
mutants lacking algicidal activity, designated NH1 and NH2, were selected after
N
-methyl-
N
′-nitrosoguanidine mutagenesis. The culture supernatants of NH1 and NH2 showed less than 15% of the protease activity detected with the parental strain, A28. The protease was purified to homogeneity from A28 culture supernatants by using ion-exchange chromatography followed by preparative gel electrophoresis. Paper-disk assays revealed that the purified protease had potent algicidal activity. The purified protease had a molecular mass for 50 kDa, and the N-terminal amino acid sequence was determined to be Ala-Thr-Pro-Asn-Asp-Pro. The optimum pH and temperature of the protease were found to be 8.8 and 30°C, respectively, by using succinyl-Ala-Ala-Pro-Phe-
p
-nitroanilide as a substrate. The protease activity was strongly inhibited by phenylmethylsulfonyl fluoride, diisopropyl fluorophosphate, antipain, chymostatin, and leupeptin. No significant inhibition was detected with EDTA, EGTA, phenanthroline or tetraethylenepentamine. These results suggest that
Pseudoalteromonas
sp. strain A28 produced an extracellular serine protease which was responsible for the algicidal activity of this marine bacterium.
Detection and Identification of Bacterial Endosymbionts in Arbuscular Mycorrhizal Fungi Belonging to the Family Gigasporaceae
Authors: Bianciotto Valeria , Lumini Erica , Lanfranco Luisa , Minerdi Daniela , Bonfante Paola , Perotto Silvia
Published: July 2002

Intracellular bacteria have been found previously in one isolate of the arbuscular mycorrhizal (AM) fungus
Gigaspora margarita
BEG 34. In this study, we extended our investigation to 11 fungal isolates obtained from different geographic areas and belonging to six different species of the family Gigasporaceae. With the exception of
Gigaspora rosea
, isolates of all of the AM species harbored bacteria, and their DNA could be PCR amplified with universal bacterial primers. Primers specific for the endosymbiotic bacteria of BEG 34 could also amplify spore DNA from four species. These specific primers were successfully used as probes for in situ hybridization of endobacteria in
G. margarita
spores. Neighbor-joining analysis of the 16S ribosomal DNA sequences obtained from isolates of
Scutellospora persica
,
Scutellospora castanea
, and
G. margarita
revealed a single, strongly supported branch nested in the genus
Burkholderia
.
A Homokaryotic Derivative of a
Phanerochaete chrysosporium
Strain and Its Use in Genomic Analysis of Repetitive Elements
Authors: Stewart Philip , Gaskell Jill , Cullen Daniel
Published: July 2002

Analysis of complex gene families in the lignin-degrading basidiomycete
Phanerochaete chrysosporium
has been hampered by the dikaryotic nuclear condition. To facilitate genetic investigations in
P. chrysosporium
strain BKM-F-1767, we isolated a homokaryon from regenerated protoplasts. The nuclear condition was established by PCR amplification of five unlinked genes followed by probing with allele-specific oligonucleotides. Under standard nitrogen-limited culture conditions, lignin peroxidase, manganese peroxidase, and glyoxal oxidase activities of the homokaryon were equivalent to those of the parental dikaryon. We used the homokaryon to determine the genomic organization and to assess transcriptional effects of a family of repetitive elements. Previous studies had identified an insertional mutation,
Pce1
, within lignin peroxidase allele
lipI2
. The element resembled nonautonomous class II transposons and was present in multiple copies in strain BKM-F-1767. In the present study, three additional copies of the
Pce1
-like element were cloned and sequenced. The distribution of elements was nonrandom; all localized to the same 3.7-Mb chromosome, as assessed by segregation analysis and Southern blot analysis of the homokaryon. Reverse transcription-PCR (RT-PCR) showed that
Pce1
was not spliced from the
lipI2
transcript in either the homokaryon or the parental dikaryon. However, both strains had equivalent lignin peroxidase activity, suggesting that some
lip
genes may be redundant.
Effect of Sample Holding Time on Recovery of
Cryptosporidium
Oocysts and
Giardia
Cysts from Water Samples
Authors: Robertson L. J. , Gjerde B.
Published: July 2002

U.S. Environmental Protection Agency methods for analysis of water for
Cryptosporidium
and
Giardia
stipulate maximum sample holding times which are not always practical to comply with. A spiking experiment indicated that holding times of up to 2 weeks had no significant effect on recovery of these parasites from 10-liter samples of raw water in plastic carboys.
Molecular Analyses of Novel Methanotrophic Communities in Forest Soil That Oxidize Atmospheric Methane
Authors: Henckel Thilo , Jäckel Udo , Schnell Sylvia , Conrad Ralf
Published: July 2002

Forest and other upland soils are important sinks for atmospheric CH4, consuming 20 to 60 Tg of CH4per year. Consumption of atmospheric CH4by soil is a microbiological process. However, little is known about the methanotrophic bacterial community in forest soils. We measured vertical profiles of atmospheric CH4oxidation rates in a German forest soil and characterized the methanotrophic populations by PCR and denaturing gradient gel electrophoresis (DGGE) with primer sets targeting thepmoAgene, coding for the α subunit of the particulate methane monooxygenase, and the small-subunit rRNA gene (SSU rDNA) of all life. The forest soil was a sink for atmospheric CH4in situ and in vitro at all times. In winter, atmospheric CH4was oxidized in a well-defined subsurface soil layer (6 to 14 cm deep), whereas in summer, the complete soil core was active (0 cm to 26 cm deep). The content of total extractable DNA was about 10-fold higher in summer than in winter. It decreased with soil depth (0 to 28 cm deep) from about 40 to 1 μg DNA per g (dry weight) of soil. The PCR product concentration of SSU rDNA of all life was constant both in winter and in summer. However, the PCR product concentration ofpmoAchanged with depth and season.pmoAwas detected only in soil layers with active CH4oxidation, i.e., 6 to 16 cm deep in winter and throughout the soil core in summer. The same methanotrophic populations were present in winter and summer. Layers with high CH4consumption rates also exhibited more bands ofpmoAin DGGE, indicating that high CH4oxidation activity was positively correlated with the number of methanotrophic populations present. ThepmoAsequences derived from excised DGGE bands were only distantly related to those of known methanotrophs, indicating the existence of unknown methanotrophs involved in atmospheric CH4consumption.
Importance of Passive Diffusion in the Uptake of Polychlorinated Biphenyls by Phagotrophic Protozoa
Authors: Kujawinski Elizabeth B. , Farrington John W. , Moffett James W.
Published: July 2002

Unicellular protozoan grazers represent a size class of organisms where a transition in the mechanism of chlorobiphenyl (CB) introduction, from diffusion through surface membranes to ingestion of contaminated prey, could occur. This study compares the relative importance of these two processes in the overall uptake of polychlorinated biphenyls by protists. Uptake rates and steady-state concentrations were compared in laboratory cultures of grazing and nongrazing protozoa. These experiments were conducted with a 10-μm marine scuticociliate (
Uronema
sp.), bacterial prey (
Halomonas halodurans
), and a suite of 21 CB congeners spanning a range of aqueous solubilities. The dominant pathway of CB uptake by both grazing and nongrazing protozoa was diffusion. Organic-carbon-normalized CB concentrations (in the protozoan cell) were equivalent in grazing and nongrazing protozoa for all congeners studied. Rate constants for uptake into and loss from the protozoan cell were independently determined by using [3,3′,4,4′-
14
C]tetrachlorobiphenyl (IUPAC no. 77), 0.38 ± 0.03 min
−1
and (1.1 ± 0.1) × 10
−5
(g of organic carbon)
−1
min
−1
, respectively. Magnitudes of the uptake and loss processes were calculated and compared by using a numerical model. The model result was consistent with data from the bioaccumulation experiment and supported the hypothesis that diffusive uptake is faster than ingestive uptake in phagotrophic unicellular protozoa.
Monitoring Precursor 16S rRNAs of
Acinetobacter
spp. in Activated Sludge Wastewater Treatment Systems
Authors: Oerther Daniel B. , Pernthaler Jakob , Schramm Andreas , Amann Rudolf , Raskin Lutgarde
Published: July 2002

Recently, Cangelosi and Brabant used oligonucleotide probes targeting the precursor 16S rRNA of
Escherichia coli
to demonstrate that the levels of precursor rRNA were more sensitive to changes in growth phase than the levels of total rRNA (G. A. Cangelosi and W. H. Brabant, J. Bacteriol. 179:4457–4463, 1997). In order to measure changes in the levels of precursor rRNA in activated sludge systems, we designed oligonucleotide probes targeting the 3′ region of the precursor 16S rRNA of
Acinetobacter
spp. We used these probes to monitor changes in the level of precursor 16S rRNA during batch growth of
Acinetobacter
spp. in Luria-Bertani (LB) medium, filtered wastewater, and in lab- and full-scale wastewater treatment systems. Consistent with the previous reports for
E. coli
, results obtained with membrane hybridizations and fluorescence in situ hybridizations with
Acinetobacter calcoaceticus
grown in LB medium showed a more substantial and faster increase in precursor 16S rRNA levels compared to the increase in total 16S rRNA levels during exponential growth. Diluting an overnight culture of
A. calcoaceticus
grown in LB medium with filtered wastewater resulted in a pattern of precursor 16S rRNA levels that appeared to follow diauxic growth. In addition, fluorescence in situ hybridizations with oligonucleotide probes targeting total 16S rRNA and precursor 16S rRNA showed that individual cells of
A. calcoaceticus
expressed highly variable levels of precursor 16S rRNA when adapting from LB medium to filtered sewage. Precursor 16S rRNA levels of
Acinetobacter
spp. transiently increased when activated sludge was mixed with influent wastewater in lab- and full-scale wastewater treatment systems. These results suggest that
Acinetobacter
spp. experience a change in growth activity within wastewater treatment systems.
Effect of Model Sorptive Phases on Phenanthrene Biodegradation: Molecular Analysis of Enrichments and Isolates Suggests Selection Based on Bioavailability
Authors: Friedrich M. , Grosser R. J. , Kern E. A. , Inskeep W. P. , Ward D. M.
Published: July 2002

Reduced bioavailability of nonpolar contaminants due to sorption to natural organic matter is an important factor controlling biodegradation of pollutants in the environment. We established enrichment cultures in which solid organic phases were used to reduce phenanthrene bioavailability to different degrees (R. J. Grosser, M. Friedrich, D. M. Ward, and W. P. Inskeep, Appl. Environ. Microbiol. 66:2695–2702, 2000). Bacteria enriched and isolated from contaminated soils under these conditions were analyzed by denaturing gradient gel electrophoresis (DGGE) and sequencing of PCR-amplified 16S ribosomal DNA segments. Compared to DGGE patterns obtained with enrichment cultures containing sand or no sorptive solid phase, different DGGE patterns were obtained with enrichment cultures containing phenanthrene sorbed to beads of Amberlite IRC-50 (AMB), a weak cation-exchange resin, and especially Biobead SM7 (SM7), a polyacrylic resin that sorbed phenanthrene more strongly. SM7 enrichments selected for mycobacterial phenanthrene mineralizers, whereas AMB enrichments selected for a
Burkholderia
sp. that degrades phenanthrene. Identical mycobacterial and
Burkholderia
16S rRNA sequence segments were found in SM7 and AMB enrichment cultures inoculated with contaminated soil from two geographically distant sites. Other closely related
Burkholderia
sp. populations, some of which utilized phenanthrene, were detected in sand and control enrichment cultures. Our results are consistent with the hypothesis that different phenanthrene-utilizing bacteria inhabiting the same soils may be adapted to different phenanthrene bioavailabilities.
Production and Characterization of Two Monoclonal Antibodies Specific for
Plasmopara halstedii
Authors: Bouterige S. , Robert R. , Bouchara J. P. , Marot-Leblond A. , Molinero V. , Senet J. M.
Published: July 2002

Sunflower downy mildew, caused by the fungus
Plasmopara halstedii
, is a potentially devastating disease. We produced two monoclonal antibodies (MAbs) (12C9 and 18E2) by immunizing mice with a partially purified extract of
P. halstedii
race 1. Both MAbs detected in enzyme-linked immunosorbent assay (ELISA) all races of
P. halstedii
present in France. No cross-reactions were observed with
Plasmopara viticola
or with other fungi commonly associated with sunflowers. Both MAbs recognized the same three fungal antigens with molecular masses of 68, 140, and 192 kDa. However, the epitopes on the fungal antigens were distinct and repetitive. Seed homogenates from infected plants were incubated in wells coated with MAb 18E2. This resulted in the trapping of
P. halstedii
antigens that were identified with biotinylated MAb 12C9. No reactions were seen with seed homogenates from healthy plants. Thus, our results suggest that these MAbs might be used to develop a sandwich ELISA detection system for
P. halstedii
in infected seeds.
Polyclonal Antibodies Recognizing the AmoB Protein of Ammonia Oxidizers of the β-Subclass of the Class
Proteobacteria
Authors: Pinck Claudia , Coeur Caroline , Potier Patrick , Bock Eberhard
Published: July 2002

A 41-kDa protein of
Nitrosomonas eutropha
was purified, and the N-terminal amino acid sequence was found to be nearly identical with the sequence of AmoB, a subunit of ammonia monooxygenase. This protein was used to develop polyclonal antibodies, which were highly specific for the detection of the four genera of ammonia oxidizers of the β-subclass of
Proteobacteria
(
Nitrosomonas
, including
Nitrosococcus mobilis
, which belongs phylogenetically to
Nitrosomonas
;
Nitrosospira
;
Nitrosolobus
; and
Nitrosovibrio
). In contrast, the antibodies did not react with ammonia oxidizers affiliated with the γ-subclass of
Proteobacteria
(
Nitrosococcus oceani
and
Nitrosococcus halophilus
). Moreover, methane oxidizers (
Methylococcus capsulatus
,
Methylocystis parvus
, and
Methylomonas methanica
) containing the related particulate methane monooxygenase were not detected. Quantitative immunoblot analysis revealed that total cell protein of
N. eutropha
consisted of approximately 6% AmoB, when cells were grown using standard conditions (mineral medium containing 10 mM ammonium). This AmoB amount was shown to depend on the ammonium concentration in the medium. About 14% AmoB of total protein was found when
N. eutropha
was grown with 1 mM ammonium, whereas 4% AmoB was detected when 100 mM ammonium were used. In addition, the cellular amount of AmoB was influenced by the absence of the substrate. Cells starved for more than 2 months contained nearly twice as much AmoB as actively growing cells, although these cells possessed low ammonia-oxidizing activity. AmoB was always present and could even be detected in cells of
Nitrosomonas
after 1 year of ammonia starvation.