bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interpretation of Genotype and Pharmacokinetics for Resistance to Fosamprenavir-Ritonavir-Based Regimens in Antiretroviral-Experienced Patients
Authors: Pellegrin Isabelle , Breilh Dominique , Coureau Gaelle , Boucher Sébastien , Neau Didier , Merel Patrick , Lacoste Denis , Fleury Hervé , Saux Marie-Claude , Pellegrin Jean-Luc , Lazaro Estibaliz , Dabis François , Thiébaut Rodolphe 
Published: February 2007

ABSTRACTIn this study, named the Zephir study (Telzir-pharmacokinetics), 121 antiretroviral-experienced human immunodeficiency virus (HIV) patients failing on highly active antiretroviral therapy (HAART) were included in a prospective cohort and received a fosamprenavir-ritonavir (700 mg/100 mg twice a day)-based regimen. The impact of baseline HIV type 1 (HIV-1) mutations, pharmacokinetic (PK) parameters, and genotype inhibitory quotient (GIQ) on the virological response at week 12 (W12) was assessed. HIV reverse transcriptase and protease were sequenced at W0. The response at W12 was defined as <2.3 log10HIV-1 RNA copies/ml or a virus load decrease of ≥1 log10copies/ml. W4 amprenavir PK were determined by high-performance liquid chromatography. Patients had a median of nine previous treatments over 8 years. Median W0 values were as follows: 295 CD4+/μl, 4.4 log10HIV-1 RNA copies/ml, and 6 protease- and 5 nucleotide reverse transcription inhibitor-related mutations. Respective values for minimum concentration of drug in serum (Cmin) and area under the concentration-time curve (AUC) from 0 to 24 h were 1,400 ng/ml and 35 mg·h/ml. At W12, 52% of the patients were successes, with a median decrease of −0.7 log10HIV-1 RNA copies/ml. The Zephir mutation score included 12 IAS protease mutations associated with poorer virological response: L10I/F/R/V, L33F, M36I, M46I/L, I54L/M/T/V, I62V, L63P, A71I/L/V/T, G73A/C/F/T, V82A/F/S/T, I84V, L90M, and polymorphism mutations I13V, L19I, K55R, and L89M. Comparing <4 versus ≥4 mutations, HIV-1 RNA decreases were −2.3 log10copies/ml versus −0.1 log10copies/ml (P< 10−4) with 93% versus 19% successes (P< 10−4), respectively. This score predicted W12 failure with 94% sensitivity, versus 31% for the ANRS 2005 algorithm.Cmin(<1,600 ng/ml), AUC (<40 mg·h/ml), and GIQ (<300) values were associated with failure (allPvalues were <10−4). The need to test genotype-based algorithms using different patient databases before their implementation in clinical practice is highlighted. Specific mutations, PK and GIQ, provide relevant information for monitoring fosamprenavir-ritonavir-based HAART.
Determination of Antibiotic Efficacy against
Bacillus anthracis
in a Mouse Aerosol Challenge Model
Authors: Heine Henry S. , Bassett Jennifer , Miller Lynda , Hartings Justin M. , Ivins Bruce E. , Pitt M. Louise , Fritz David , Norris Sarah L. , Byrne W. Russell 
Published: February 2007

ABSTRACT

An anthrax spore aerosol infection mouse model was developed as a first test of in vivo efficacy of antibiotics identified as active against
Bacillus anthracis
. Whole-body, 50% lethal dose (LD
50
) aerosol challenge doses in a range of 1.9 × 10
3
to 3.4 × 10
4
CFU with spores of the fully virulent Ames strain were established for three inbred and one outbred mouse strain (A/J, BALB/c, C57BL, and Swiss Webster). The BALB/c strain was further developed as a model for antibiotic efficacy. Time course microbiological examinations of tissue burdens in mice after challenge showed that spores could remain dormant in the lungs while vegetative cells disseminated to the mediastinal lymph nodes and then to the spleen, accompanied by bacteremia. For antibiotic efficacy studies, BALB/c mice were challenged with 50 to 100 LD
50
of spores followed by intraperitoneal injection of either ciprofloxacin at 30 mg/kg of body weight (every 12 h [q12h]) or doxycycline at 40 mg/kg (q6h). A control group was treated with phosphate-buffered saline (PBS) q6h. Treatment was begun 24 h after challenge with groups of 10 mice for 14 or 21 days. The PBS-treated control mice all succumbed (10/10) to inhalation anthrax infection within 72 h. Sixty-day survival rates for ciprofloxacin and doxycycline-treated groups were 8/10 and 9/10, respectively, for 14-day treatment and 10/10 and 7/10 for 21-day treatment. Delayed treatment with ciprofloxacin initiated 36 and 48 h postexposure resulted in 80% survival and was statistically no different than early (24 h) postexposure treatment. Results using this mouse model correlate closely with clinical observations of inhalational anthrax in humans and with earlier antibiotic studies in the nonhuman primate inhalational anthrax model.
Phylogenetic Analysis of Bacteria Preserved in a Permafrost Ice Wedge for 25,000 Years
Authors: Katayama Taiki , Tanaka Michiko , Moriizumi Jun , Nakamura Toshio , Brouchkov Anatoli , Douglas Thomas A. , Fukuda Masami , Tomita Fusao , Asano Kozo 
Published: February 2007

ABSTRACTPhylogenetic analysis of bacteria preserved within an ice wedge from the Fox permafrost tunnel was undertaken by cultivation and molecular techniques. The radiocarbon age of the ice wedge was determined. Our results suggest that the bacteria in the ice wedge adapted to the frozen conditions have survived for 25,000 years.
Carbohydrate Starvation Causes a Metabolically Active but Nonculturable State in
Lactococcus lactis
Authors: Ganesan Balasubramanian , Stuart Mark R. , Weimer Bart C. 
Published: February 2007

ABSTRACT
This study characterized the ability of lactococci to become nonculturable under carbohydrate starvation while maintaining metabolic activity. We determined the changes in physiological parameters and extracellular substrate levels of multiple lactococcal strains under a number of environmental conditions along with whole-genome expression profiles. Three distinct phases were observed, logarithmic growth, sugar exhaustion, and nonculturability. Shortly after carbohydrate starvation, each lactococcal strain lost the ability to form colonies on solid media but maintained an intact cell membrane and metabolic activity for over 3.5 years. ML3, a strain that metabolized lactose rapidly, reached nonculturability within 1 week. Strains that metabolized lactose slowly (SK11) or not at all (IL1403) required 1 to 3 months to become nonculturable. In all cases, the cells contained at least 100 pM of intracellular ATP after 6 months of starvation and remained at that level for the remainder of the study. Aminopeptidase and lipase/esterase activities decreased below detection limits during the nonculturable phase. During sugar exhaustion and entry into nonculturability, serine and methionine were produced, while glutamine and arginine were depleted from the medium. The cells retained the ability to transport amino acids via proton motive force and peptides via ATP-driven translocation. The addition of branched-chain amino acids to the culture medium resulted in increased intracellular ATP levels and new metabolic products, indicating that branched-chain amino acid catabolism resulted in energy and metabolic products to support survival during starvation. Gene expression analysis showed that the genes responsible for sugar metabolism were repressed as the cells entered nonculturability. The genes responsible for cell division were repressed, while autolysis and cell wall metabolism genes were induced neither at starvation nor during nonculturability. Taken together, these observations verify that carbohydrate-starved lactococci attain a nonculturable state wherein sugar metabolism, cell division, and autolysis are repressed, allowing the cells to maintain transcription, metabolic activity, and energy production during a state that produces new metabolites not associated with logarithmic growth.
Succession and Diel Transcriptional Response of the Glycolate-Utilizing Component of the Bacterial Community during a Spring Phytoplankton Bloom
Authors: Lau Winnie W. Y. , Keil Richard G. , Armbrust E. Virginia 
Published: February 2007

ABSTRACT

The influence of the phytoplankton-specific organic compound glycolate on bacterial community structure was examined during the 2004 spring phytoplankton bloom (February to April) in Dabob Bay in Washington. The diversity of the bacteria able to utilize glycolate during the phytoplankton bloom was determined using previously developed PCR primers to amplify the gene for the D subunit of glycolate oxidase (
glcD
). Many of the
glcD
sequences obtained represented novel sequences that appeared to be specific to marine environments. Overall, the
glcD
sequence diversity decreased as the phytoplankton bloom progressed. Phylotype-specific
glcD
quantitative PCR primers were designed for the six most commonly detected
glcD
phylotypes that represented distinct phylogenetic groups of heterotrophic bacteria. Three patterns of phylotype abundance were detected: four phylotypes were most abundant during the onset of the bloom; the abundance of one phylotype increased as the bloom progressed; and one phylotype was abundant throughout the bloom. Quantitative reverse transcriptase PCR with the same phylotype-specific primers was used to determine the levels of day and night
glcD
RNA transcription over the course of the bloom.
glcD
transcripts, when detectable, were always more abundant in the day than at night for each phylotype, suggesting that the bacteria responded to the glycolate produced by phytoplankton during the day. The nearly constant low in situ glycolate concentrations suggested that bacteria rapidly utilized the available glycolate. This study provided evidence for direct phytoplankton-bacterium interactions and the resulting succession in a single functional group of marine bacteria.
Gamma Study of pH, Nitrite, and Salt Inhibition of
Aeromonas hydrophila
Authors: Lambert Ronald J. W. , Bidlas Eva 
Published: February 2007

ABSTRACT

The gamma hypothesis states that there are no interactions between antimicrobial environmental factors. The time to growth of
Aeromonas hydrophila
challenged with pH, NaNO
2
, and salt combinations at 30°C was investigated. Data were examined using a model based on the gamma hypothesis (the gamma model), which takes into account variance-stabilizing transformations and which gives biologically relevant parameters. At high concentrations of NaNO
2
and at pHs of >6.0, the antimicrobial action of the nitrite ion has a strong influence (MIC = 2,033 mg liter
−1
), whereas at pHs of <6, nitrous acid is dominant (MIC = 1.5 mg liter
−1
). This change is not due to a “synergy” between pH and the nitrite ion but is due to the shift in the equilibrium concentrations of nitrous acid and nitrite in solution caused by pH. In combination with salt, the parameters found for the action of Na nitrite were identical to those found when it was examined in isolation. Therefore, pH, NaNO
2
, and salt act independently on the growth of
A. hydrophila
. By expanding the gamma model with a cardinal temperature model, the results of fitting the model of Palumbo et al. (J. Food Prot.
54:
429-435, 1994) to randomly produced environmental conditions could be reproduced, suggesting that temperature also has an independent effect.
Detection of Low-Copy-Number Genomic DNA Sequences in Individual Bacterial Cells by Using Peptide Nucleic Acid-Assisted Rolling-Circle Amplification and Fluorescence In Situ Hybridization
Authors: Smolina Irina , Lee Charles , Frank-Kamenetskii Maxim 
Published: February 2007

ABSTRACTAn approach is proposed for in situ detection of short signature DNA sequences present in single copies per bacterial genome. The site is locally opened by peptide nucleic acids, and a circular oligonucleotide is assembled. The amplicon generated by rolling circle amplification is detected by hybridization with fluorescently labeled decorator probes.
Isolation and Characterization of Soil Bacteria That Define
Terriglobus
gen. nov., in the Phylum
Acidobacteria
Authors: Eichorst Stephanie A. , Breznak John A. , Schmidt Thomas M. 
Published: February 2007

ABSTRACT

Bacteria in the phylum
Acidobacteria
are widely distributed and abundant in soils, but their ecological roles are poorly understood, owing in part to a paucity of cultured representatives. In a molecular survey of acidobacterial diversity at the Michigan State University Kellogg Biological Station Long-Term Ecological Research site, 27% of acidobacterial 16S rRNA gene clones in a never-tilled, successional plant community belonged to subdivision 1, whose relative abundance varied inversely with soil pH. Strains of subdivision 1 were isolated from these never-tilled soils using low-nutrient medium incubated for 3 to 4 weeks under elevated levels of carbon dioxide, which resulted in a slightly acidified medium that matched the pH optima of the strains (between 5 and 6). Colonies were approximately 1 mm in diameter and either white or pink, the latter due to a carotenoid(s) that was synthesized preferentially under 20% instead of 2% oxygen. Strains were gram-negative, aerobic, chemo-organotrophic, nonmotile rods that produced an extracellular matrix. All strains contained either one or two copies of the 16S rRNA encoding gene, which along with a relatively slow doubling time (10 to 15 h at ca. 23°C) is suggestive of an oligotrophic lifestyle. Six of the strains are sufficiently similar to one another, but distinct from previously named
Acidobacteria
, to warrant creation of a new genus,
Terriglobus
, with
Terriglobus roseus
defined as the type species. The physiological and nutritional characteristics of
Terriglobus
are consistent with its potential widespread distribution in soil.
Cellular Identification of a Novel Uncultured Marine Stramenopile (MAST-12 Clade) Small-Subunit rRNA Gene Sequence from a Norwegian Estuary by Use of Fluorescence In Situ Hybridization-Scanning Electron Microscopy
Authors: Kolodziej Karolina , Stoeck Thorsten 
Published: February 2007

ABSTRACT

Revealing the cellular identity of organisms behind environmental eukaryote rRNA gene sequences is a major objective in microbial diversity research. We sampled an estuarine oxygen-depleted microbial mat in southwestern Norway and retrieved an 18S rRNA gene signature that branches in the MAST-12 clade, an environmental marine stramenopile clade. Detailed phylogenetic analyses revealed that MAST-12 branches among the heterotrophic stramenopiles as a sister of the free-living Bicosoecida and the parasitic genus
Blastocystis
. Specific sequence signatures confirmed a relationship to these two groups while excluding direct assignment. We designed a specific oligonucleotide probe for the target sequence and detected the corresponding organism in incubation samples using fluorescence in situ hybridization (FISH). Using the combined FISH-scanning electron microscopy approach (T. Stoeck, W. H. Fowle, and S. S. Epstein, Appl. Environ. Microbiol.
69:
6856-6863, 2003), we determined the morphotype of the target organism among the very diverse possible morphologies of the heterotrophic stramenopiles. The unpigmented cell is spherical and about 5 μm in diameter and possesses a short flagellum and a long flagellum, both emanating anteriorly. The long flagellum bears mastigonemes in a characteristic arrangement, and its length (30 μm) distinguishes the target organism from other recognized heterotrophic stramenopiles. The short flagellum is naked and often directed posteriorly. The organism possesses neither a lorica nor a stalk. The morphological characteristics that we discovered should help isolate a representative of a novel stramenopile group, possibly at a high taxonomic level, in order to study its ultrastructure, physiological capabilities, and ecological role in the environment.
Campylobacter jejuni
Strains Compete for Colonization in Broiler Chicks
Authors: Konkel Michael E. , Christensen Jeffrey E. , Dhillon A. Singh , Lane Alison B. , Hare-Sanford Rebekah , Schaberg Dennis M. , Larson Charles L. 
Published: February 2007

ABSTRACT

Campylobacter jejuni
isolates possess multiple adhesive proteins termed adhesins, which promote the organism's attachment to epithelial cells. Based on the proposal that one or more adhesins are shared among
C. jejuni
isolates, we hypothesized that
C. jejuni
strains would compete for intestinal and cecal colonization in broiler chicks. To test this hypothesis, we selected two
C. jejuni
strains with unique SmaI pulsed-field gel electrophoresis macrorestriction profiles and generated one nalidixic acid-resistant strain (the F38011 Nal
r
strain) and one streptomycin-resistant strain (the 02-833L Str
r
strain). In vitro binding assays revealed that the
C. jejuni
F38011 Nal
r
and 02-833L Str
r
strains adhered to LMH chicken hepatocellular carcinoma epithelial cells and that neither strain influenced the binding potential of the other strain at low inoculation doses. However, an increase in the dose of the
C. jejuni
02-833L Str
r
strain relative to that of the
C. jejuni
F38011 Nal
r
strain competitively inhibited the binding of the
C. jejuni
F38011 Nal
r
strain to LMH cells in a dose-dependent fashion. Similarly, the
C. jejuni
02-833L Str
r
strain was found to significantly reduce the efficiency of intestinal and cecal colonization by the
C. jejuni
F38011 Nal
r
strain in broiler chickens. Based on the number of bacteria recovered from the ceca, the maximum number of bacteria that can colonize the digestive tracts of chickens may be limited by host constraints. Collectively, these data support the hypothesis that
C. jejuni
strains compete for colonization in chicks and suggest that it may be possible to design novel intervention strategies for reducing the level at which
C. jejuni
colonizes the cecum.
Reaerosolization of Fluidized Spores in Ventilation Systems
Authors: Krauter Paula , Biermann Arthur 
Published: February 2007

ABSTRACT

This project examined dry, fluidized spore reaerosolization in a heating, ventilating, and air conditioning duct system. Experiments using spores of
Bacillus atrophaeus
, a nonpathogenic surrogate for
Bacillus anthracis
, were conducted to delineate the extent of spore reaerosolization behavior under normal indoor airflow conditions. Short-term (five air-volume exchanges), long-term (up to 21,000 air-volume exchanges), and cycled (on-off) reaerosolization tests were conducted using two common duct materials. Spores were released into the test apparatus in turbulent airflow (Reynolds number, 26,000). After the initial pulse of spores (approximately 10
10
to 10
11
viable spores) was released, high-efficiency particulate air filters were added to the air intake. Airflow was again used to perturb the spores that had previously deposited onto the duct. Resuspension rates on both steel and plastic duct materials were between 10
−3
and 10
−5
per second, which decreased to 10 times less than initial rates within 30 min. Pulsed flow caused an initial spike in spore resuspension concentration that rapidly decreased. The resuspension rates were greater than those predicted by resuspension models for contamination in the environment, a result attributed to surface roughness differences. There was no difference between spore reaerosolization from metal and that from plastic duct surfaces over 5 hours of constant airflow. The spores that deposited onto the duct remained a persistent source of contamination over a period of several hours.
Salt-Inducible Bionylon Polymer from
Bacillus megaterium
Authors: Shimizu Kazuki , Nakamura Hisaaki , Ashiuchi Makoto 
Published: February 2007

ABSTRACT

Poly-γ-glutamate (PGA) is a chiral polyamide material that possesses a nylon-like backbone, a bionylon polymer. We examined the PGA productivity of
Bacillus megaterium
and found NaCl-responsive PGA production in the bacterium. In the system of
B. megaterium
, salt would be significant in controlling the yield, molecular size, and stereochemistry of bionylon.
Potential for Mercury Reduction by Microbes in the High Arctic
Authors: Poulain Alexandre J. , Ní Chadhain Sinéad M. , Ariya Parisa A. , Amyot Marc , Garcia Edenise , Campbell Peter G. C. , Zylstra Gerben J. , Barkay Tamar 
Published: February 2007

ABSTRACT

The contamination of polar regions due to the global distribution of anthropogenic pollutants is of great concern because it leads to the bioaccumulation of toxic substances, methylmercury among them, in Arctic food chains. Here we present the first evidence that microbes in the high Arctic possess and express diverse
merA
genes, which specify the reduction of ionic mercury [Hg(II)] to the volatile elemental form [Hg(0)]. The sampled microbial biomass, collected from microbial mats in a coastal lagoon and from the surface of marine macroalgae, was comprised of bacteria that were most closely related to psychrophiles that had previously been described in polar environments. We used a kinetic redox model, taking into consideration photoredox reactions as well as
mer
-mediated reduction, to assess if the potential for Hg(II) reduction by Arctic microbes can affect the toxicity and environmental mobility of mercury in the high Arctic. Results suggested that
mer
-mediated Hg(II) reduction could account for most of the Hg(0) that is produced in high Arctic waters. At the surface, with only 5% metabolically active cells, up to 68% of the mercury pool was resolved by the model as biogenic Hg(0). At a greater depth, because of incident light attenuation, the significance of photoredox transformations declined and
merA
-mediated activity could account for up to 90% of Hg(0) production. These findings highlight the importance of microbial redox transformations in the biogeochemical cycling, and thus the toxicity and mobility, of mercury in polar regions.
l
-Valine Production with Pyruvate Dehydrogenase Complex-Deficient
Corynebacterium glutamicum
Authors: Blombach Bastian , Schreiner Mark E. , Holátko Jiří , Bartek Tobias , Oldiges Marco , Eikmanns Bernhard J. 
Published: February 2007

ABSTRACT

Corynebacterium glutamicum
was engineered for the production of
l
-valine from glucose by deletion of the
aceE
gene encoding the E1p enzyme of the pyruvate dehydrogenase complex and additional overexpression of the
ilvBNCE
genes encoding the
l
-valine biosynthetic enzymes acetohydroxyacid synthase, isomeroreductase, and transaminase B. In the absence of cellular growth,
C. glutamicum
Δ
aceE
showed a relatively high intracellular concentration of pyruvate (25.9 mM) and produced significant amounts of pyruvate,
l
-alanine, and
l
-valine from glucose as the sole carbon source. Lactate or acetate was not formed. Plasmid-bound overexpression of
ilvBNCE
in
C. glutamicum
Δ
aceE
resulted in an approximately 10-fold-lower intracellular pyruvate concentration (2.3 mM) and a shift of the extracellular product pattern from pyruvate and
l
-alanine towards
l
-valine. In fed-batch fermentations at high cell densities and an excess of glucose,
C. glutamicum
Δ
aceE
(pJC4ilvBNCE) produced up to 210 mM
l
-valine with a volumetric productivity of 10.0 mM h
−1
(1.17 g l
−1
h
−1
) and a maximum yield of about 0.6 mol per mol (0.4 g per g) of glucose.