bluuebunny/crossref_metadata_2025_split huggingface dataset:
Steady‐state nevirapine plasma concentrations are influenced by pregnancy
Authors: Nellen JFJB , Damming M , Godfried MH , Boer K , Van Der Ende ME , Burger DM , De Wolf F , Wit FWNM , Prins JM 
Published: March 2008

ObjectivesOptimal plasma concentrations of antiretroviral drugs are required during pregnancy to treat maternal HIV infection and prevent mother‐to‐child transmission. We investigated the effect of pregnancy on nevirapine (NVP) plasma concentrations.MethodsWe included all HIV‐1‐infected women for whom NVP plasma concentrations were available as part of routine patient care at two university hospitals. Plasma NVP concentrations were compared for pregnant (n=45) and non‐pregnant (n=152) women. Univariate and multivariate linear regression analyses were used to identify and adjust for other confounding factors associated with NVP plasma concentrations. For pregnant women who had a plasma NVP concentration available both during and outside pregnancy, a paired analysis was performed.ResultsSteady‐state NVP plasma concentrations were lower in pregnant women: 5.2 mg/L (interquartile range 3.9–6.8)vs.5.8 mg/L (4.3–7.7) (P=0.08). After adjusting for confounders, both pregnancy (regression coefficient=–0.90 mg/L,P=0.046) and African descent (regression coefficient=+1.13 mg/L,P=0.005) influenced NVP concentrations significantly. The paired analysis showed mean concentrations of 4.8 mg/L during pregnancy and 5.8 mg/L outside pregnancy (pairedt‐test,P=0.073).ConclusionsPregnancy has a moderate but significant lowering effect on NVP plasma concentrations. Being of African descent compensates for the lowering effect of pregnancy on NVP concentrations.
Hepatotoxicity of nevirapine in virologically suppressed patients according to gender and CD4 cell counts*
Authors: De Lazzari E , León A , Arnaiz JA , Martinez E , Knobel H , Negredo E , Clotet B , Montaner J , Storfer S , Asenjo MA , Mallolas J , Miró JM , Gatell JM 
Published: March 2008

ObjectivesA warning advising a higher risk of hepatotoxicity in antiretroviral‐naive patients starting a nevirapine‐containing combination antiretroviral therapy (NcART) has been issued by health authorities. It is unclear whether this higher risk also applies to stable virologically suppressed patients starting NcART.MethodsWe performed a meta‐analysis of published randomized studies including virologically suppressed patients who switched to NcART with a follow‐up ≥3 months. CD4 cell cell counts were classified as high (HCD4) (400 cells/μL for males and 250 cells/μL for females) or low (LCD4). The main endpoint was hepatotoxicity within the first 3 months.ResultsFour studies with a pooled total of 410 patients were included. The risk of hepatotoxicity within the first 3 months was 2% and 4% in the LCD4 and HCD4 groups, respectively, with a combined odds ratio of 1.46 [95% confidence interval (CI) 0.43–4.98; P=0.54]. The risk of hepatotoxicity at any point during the study was similar in both groups, with a combined hazard ratio of 0.8 (95% CI 0.3–2.5; P=0.80).ConclusionsIn our study, virologically suppressed patients switching to nevirapine did not have a significantly higher risk of hepatotoxicity or rash when stratified by gender and CD4 cell count, although small differences may have gone undetected because of the sample size limitation.
Knowledge of their children's HIV status in HIV‐positive mothers attending a genitourinary medicine clinic in the UK
Authors: Eisenhut M , Sharma V , Kawsar M , Balachandran T 
Published: March 2008

ObjectivesTo determine whether HIV‐infected mothers knew the HIV status of their children, enabling the offer of targeted testing of children at risk.MethodsAll HIV‐positive women attending the genitourinary medicine clinic at a district general hospital in the United Kingdom were asked whether they had children and the age, HIV status and residence of their children using a standardized proforma.ResultsA total of 297 HIV‐positive women were included in a prospective audit. Two hundred and fifty‐four women had 551 offspring; 143 had a total of 217 children aged <16 years. Of those children, 118 lived in the United Kingdom. Of the 99 children living abroad, 71% were living in Zimbabwe, 21% in other African countries (Zambia, Kenya, Burundi, Malawi and South Africa) and 5% in Jamaica and other Caribbean countries. Of the 118 children living in the UK, mothers knew the HIV status in 49 (42%), of whom nine (18%) were HIV positive. A further two older offspring were also HIV positive. Mothers were aware of the HIV status in significantly fewer children staying in the country of origin: nine (9%; P<0.05), of whom four were known to be HIV positive. All HIV‐positive children living in the United Kingdom were under the care of paediatricians with special expertise in paediatric HIV infection.ConclusionsThe HIV status of the majority of children of HIV‐positive immigrant mothers is unknown, particularly those children who remain in their country of origin.
Effect of aging on neurogenesis in the canine brain
Authors: Pekcec Anton , Baumgärtner Wolfgang , Bankstahl Jens P. , Stein Veronika M. , Potschka Heidrun 
Published: March 2008

SummaryAn age‐dependent decline in hippocampal neurogenesis has been reported in laboratory rodents. Environmental enrichment proved to be a strong trigger of neurogenesis in young and aged laboratory rodents, which are generally kept in facilities with a paucity of environmental stimuli. These data raise the question whether an age‐dependent decline in hippocampal cell proliferation and neurogenesis can also be observed in individuals exposed to diversified and varying surroundings. Therefore, we determined rates of canine hippocampal neurogenesis using post‐mortem tissue from 37 nonlaboratory dogs that were exposed to a variety of environmental conditions throughout their life. Expression of the neuronal progenitor cell marker doublecortin clearly correlated with age. The analysis of doublecortin‐labeled cells in dogs aged > 133 months indicated a 96% drop in the aged canine brain as compared to young adults. Expression of the proliferation marker Ki‐67 in the subgranular zone decreased until dogs were aged 85–132 months. In the aging canine brain amyloid‐beta peptide deposits have been described that might resemble an early pathophysiological change in the course of human Alzheimer's disease. Comparison of Ki‐67 and doublecortin expression in canine brain tissue with or without diffuse plaques revealed no differences. The data indicate that occurrence of diffuse plaques in the aging brain is not sufficient to trigger enhanced proliferation or enhanced neurogenesis such as described in human Alzheimer's disease. In addition, this study gives first proof that an age‐dependent decline also dominates hippocampal neurogenesis rates in individuals living in diversified environments.
Characterization and Growth of Polymorphic
Rickettsia felis
in a Tick Cell Line
Authors: Sunyakumthorn Piyanate , Bourchookarn Apichai , Pornwiroon Walairat , David Connie , Barker Steven A. , Macaluso Kevin R. 
Published: March 2008

ABSTRACT

Morphological differentiation in some arthropod-borne bacteria is correlated with increased bacterial virulence, transmission potential, and/or as a response to environmental stress. In the current study, we utilized an in vitro model to examine
Rickettsia felis
morphology and growth under various culture conditions and bacterial densities to identify potential factors that contribute to polymorphism in rickettsiae. We utilized microscopy (electron microscopy and immunofluorescence), genomic (PCR amplification and DNA sequencing of rickettsial genes), and proteomic (Western blotting and liquid chromatography-tandem mass spectrometry) techniques to identify and characterize morphologically distinct, long-form
R. felis
. Without exchange of host cell growth medium, polymorphic
R. felis
was detected at 12 days postinoculation when rickettsiae were seeded at a multiplicity of infection (MOI) of 5 and 50. Compared to short-form
R. felis
organisms, no change in membrane ultrastructure in long-form polymorphic rickettsiae was observed, and rickettsiae were up to six times the length of typical short-form rickettsiae. In vitro assays demonstrated that short-form
R. felis
entered into and replicated in host cells faster than long-form
R. felis
. However, when both short- and long-form
R. felis
organisms were maintained in cell-free medium for 12 days, the infectivity of short-form
R. felis
was decreased compared to long-form
R. felis
organisms, which were capable of entering host cells, suggesting that long-form
R. felis
is more stable outside the host cell. The relationship between rickettsial polymorphism and rickettsial survivorship should be examined further as the yet undetermined route of horizontal transmission of
R. felis
may utilize metabolically and morphologically distinct forms for successful transmission.
Linking Microbial Phylogeny to Metabolic Activity at the Single-Cell Level by Using Enhanced Element Labeling-Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (EL-FISH) and NanoSIMS
Authors: Behrens Sebastian , Lösekann Tina , Pett-Ridge Jennifer , Weber Peter K. , Ng Wing-On , Stevenson Bradley S. , Hutcheon Ian D. , Relman David A. , Spormann Alfred M. 
Published: March 2008

ABSTRACT

To examine phylogenetic identity and metabolic activity of individual cells in complex microbial communities, we developed a method which combines rRNA-based in situ hybridization with stable isotope imaging based on nanometer-scale secondary-ion mass spectrometry (NanoSIMS). Fluorine or bromine atoms were introduced into cells via 16S rRNA-targeted probes, which enabled phylogenetic identification of individual cells by NanoSIMS imaging. To overcome the natural fluorine and bromine backgrounds, we modified the current catalyzed reporter deposition fluorescence in situ hybridization (FISH) technique by using halogen-containing fluorescently labeled tyramides as substrates for the enzymatic tyramide deposition. Thereby, we obtained an enhanced element labeling of microbial cells by FISH (EL-FISH). The relative cellular abundance of fluorine or bromine after EL-FISH exceeded natural background concentrations by up to 180-fold and allowed us to distinguish target from non-target cells in NanoSIMS fluorine or bromine images. The method was optimized on single cells of axenic
Escherichia coli
and
Vibrio cholerae
cultures. EL-FISH/NanoSIMS was then applied to study interrelationships in a dual-species consortium consisting of a filamentous cyanobacterium and a heterotrophic alphaproteobacterium. We also evaluated the method on complex microbial aggregates obtained from human oral biofilms. In both samples, we found evidence for metabolic interactions by visualizing the fate of substrates labeled with
13
C-carbon and
15
N-nitrogen, while individual cells were identified simultaneously by halogen labeling via EL-FISH. Our novel approach will facilitate further studies of the ecophysiology of known and uncultured microorganisms in complex environments and communities.
Concentration of Enteroviruses, Adenoviruses, and Noroviruses from Drinking Water by Use of Glass Wool Filters
Authors: Lambertini Elisabetta , Spencer Susan K. , Bertz Phillip D. , Loge Frank J. , Kieke Burney A. , Borchardt Mark A. 
Published: March 2008

ABSTRACT

Available filtration methods to concentrate waterborne viruses are either too costly for studies requiring large numbers of samples, limited to small sample volumes, or not very portable for routine field applications. Sodocalcic glass wool filtration is a cost-effective and easy-to-use method to retain viruses, but its efficiency and reliability are not adequately understood. This study evaluated glass wool filter performance to concentrate the four viruses on the U.S. Environmental Protection Agency contaminant candidate list, i.e., coxsackievirus, echovirus, norovirus, and adenovirus, as well as poliovirus. Total virus numbers recovered were measured by quantitative reverse transcription-PCR (qRT-PCR); infectious polioviruses were quantified by integrated cell culture (ICC)-qRT-PCR. Recovery efficiencies averaged 70% for poliovirus, 14% for coxsackievirus B5, 19% for echovirus 18, 21% for adenovirus 41, and 29% for norovirus. Virus strain and water matrix affected recovery, with significant interaction between the two variables. Optimal recovery was obtained at pH 6.5. No evidence was found that water volume, filtration rate, and number of viruses seeded influenced recovery. The method was successful in detecting indigenous viruses in municipal wells in Wisconsin. Long-term continuous filtration retained viruses sufficiently for their detection for up to 16 days after seeding for qRT-PCR and up to 30 days for ICC-qRT-PCR. Glass wool filtration is suitable for large-volume samples (1,000 liters) collected at high filtration rates (4 liters min
−1
), and its low cost makes it advantageous for studies requiring large numbers of samples.
Assessment of the Genetic Diversity of
Xanthomonas axonopodis
pv. phaseoli and
Xanthomonas fuscans
subsp.
fuscans
as a Basis To Identify Putative Pathogenicity Genes and a Type III Secretion System of the SPI-1 Family by Multiple Suppression Subtractive Hybridizations
Authors: Alavi Seyed Mehdi , Sanjari Saeideh , Durand Fabien , Brin Chrystelle , Manceau Charles , Poussier Stéphane 
Published: March 2008

ABSTRACT

Fluorescent amplified fragment length polymorphism revealed that strains of
Xanthomonas axonopodis
pv. phaseoli and
Xanthomonas fuscans
subsp.
fuscans
are genetically distinct and can be grouped into four genetic lineages. Four suppression subtractive hybridizations were then performed to isolate DNA fragments present in these bean pathogens and absent from closely related xanthomonads. Virulence gene candidates were identified such as homologs of hemagglutinins, TonB-dependent receptors, zinc-dependent metalloproteases, type III effectors, and type IV secretion system components. Unexpectedly, homologs of the type III secretion apparatus components (SPI-1 family), usually reported in animal pathogens and insect symbionts, were also detected.
Recovery, Purification, and Cloning of High-Molecular-Weight DNA from Soil Microorganisms
Authors: Liles Mark R. , Williamson Lynn L. , Rodbumrer Jitsupang , Torsvik Vigdis , Goodman Robert M. , Handelsman Jo 
Published: March 2008

ABSTRACT
We describe here an improved method for isolating, purifying, and cloning DNA from diverse soil microbiota. Soil microorganisms were extracted from soils and embedded and lysed within an agarose plug. Nucleases that copurified with the metagenomic DNA were removed by incubating plugs with a high-salt and -formamide solution. This method was used to construct large-insert soil metagenomic libraries.
Isolation of the Exoelectrogenic Bacterium
Ochrobactrum anthropi
YZ-1 by Using a U-Tube Microbial Fuel Cell
Authors: Zuo Yi , Xing Defeng , Regan John M. , Logan Bruce E. 
Published: March 2008

ABSTRACT

Exoelectrogenic bacteria have potential for many different biotechnology applications due to their ability to transfer electrons outside the cell to insoluble electron acceptors, such as metal oxides or the anodes of microbial fuel cells (MFCs). Very few exoelectrogens have been directly isolated from MFCs, and all of these organisms have been obtained by techniques that potentially restrict the diversity of exoelectrogenic bacteria. A special U-tube-shaped MFC was therefore developed to enrich exoelectrogenic bacteria with isolation based on dilution-to-extinction methods. Using this device, we obtained a pure culture identified as
Ochrobactrum anthropi
YZ-1 based on 16S rRNA gene sequencing and physiological and biochemical characterization. Strain YZ-1 was unable to respire using hydrous Fe(III) oxide but produced 89 mW/m
2
using acetate as the electron donor in the U-tube MFC. Strain YZ-1 produced current using a wide range of substrates, including acetate, lactate, propionate, butyrate, glucose, sucrose, cellobiose, glycerol, and ethanol. Like another exoelectrogenic bacterium (
Pseudomonas aeruginosa
),
O. anthropi
is an opportunistic pathogen, suggesting that electrogenesis should be explored as a characteristic that confers advantages to these types of pathogenic bacteria. Further applications of this new U-tube MFC system should provide a method for obtaining additional exoelectrogenic microorganisms that do not necessarily require metal oxides for cell respiration.
Regulation of Thermotolerance by Stress-Induced Transcription Factors in
Saccharomyces cerevisiae
Authors: Yamamoto Noritaka , Maeda Yuka , Ikeda Aya , Sakurai Hiroshi 
Published: March 2008

ABSTRACT

The heat shock transcription factor Hsf1 and the general stress transcription factors Msn2 and Msn4 (Msn2/4) are major regulators of the heat shock response in
Saccharomyces cerevisiae
. Here, we show that transcriptional activation of their target genes, including
HSP104
, an antistress chaperone gene, is obligatory for thermotolerance. Although Hsf1 activity might be necessary before the exposure of cells to high temperature, severe heat shock induced the binding of hyperphosphorylated Hsf1 to its target promoters. However, promoter-bound, phosphorylated Hsf1 was inactive for transcription because RNA polymerase II was inactive at high temperatures. Rather, our results suggest that Hsf1 activates the transcription of most of its target genes during the recovery period following severe heat shock. This delayed upregulation by Hsf1, which would be induced by misfolded proteins that accumulate in severely heat-shocked cells, is required for the resumption of normal cell growth. In contrast, the factors Msn2/4 were not involved in the delayed upregulation of genes and were dispensable for cell growth during the recovery period, suggesting that they play a role before the exposure to high temperature. These results show that Hsf1 and Msn2/4 act differentially before and after exposure to extreme temperatures to ensure cell survival and growth.
Regulation of Gene Expression in a Mixed-Genus Community: Stabilized Arginine Biosynthesis inStreptococcus gordoniiby Coaggregation withActinomyces naeslundii
Authors: Jakubovics Nicholas S. , Gill Steven R. , Iobst Stacey E. , Vickerman M. M. , Kolenbrander Paul E. 
Published: March 2008

ABSTRACTInteractions involving genetically distinct bacteria, for example, between oral streptococci and actinomyces, are central to dental plaque development. A DNA microarray identifiedStreptococcus gordoniigenes regulated in response to coaggregation withActinomyces naeslundii. The expression of 23 genes changed >3-fold in coaggregates, including that of 9 genes involved in arginine biosynthesis and transport. The capacity ofS. gordoniito synthesize arginine was assessed using a chemically defined growth medium. In monoculture, streptococcal arginine biosynthesis was inefficient and streptococci could not grow aerobically at low arginine concentrations. In dual-species cultures containing coaggregates, however,S. gordoniigrew to high cell density at low arginine concentrations. Equivalent cocultures without coaggregates showed no growth until coaggregation was evident (9 h). AnargHmutant was unable to grow at low arginine concentrations with or withoutA. naeslundii, indicating that arginine biosynthesis was essential for coaggregation-induced streptococcal growth. Using quantitative reverse transcriptase PCR, the expression ofargC,argG, andpyrAbwas strongly (10- to 100-fold) up-regulated inS. gordoniimonocultures after 3 h of growth when exogenous arginine was depleted. Cocultures without induced coaggregation showed similar regulation. However, within 1 h after coaggregation withA. naeslundii, the expression ofargC,argG, andpyrAbinS. gordoniiwas partially up-regulated although arginine was plentiful, and mRNA levels did not increase further when arginine was diminished. Thus,A. naeslundiistabilizesS. gordoniiexpression of arginine biosynthesis genes in coaggregates but not cocultures and enables aerobic growth when exogenous arginine is limited.
Phylogenetic Analysis of the Incidence ofluxGene Horizontal Transfer inVibrionaceae
Authors: Urbanczyk Henryk , Ast Jennifer C. , Kaeding Allison J. , Oliver James D. , Dunlap Paul V. 
Published: March 2008

ABSTRACTHorizontal gene transfer (HGT) is thought to occur frequently in bacteria in nature and to play an important role in bacterial evolution, contributing to the formation of new species. To gain insight into the frequency of HGT inVibrionaceaeand its possible impact on speciation, we assessed the incidence of interspecies transfer of theluxgenes (luxCDABEG), which encode proteins involved in luminescence, a distinctive phenotype. Three hundred three luminous strains, most of which were recently isolated from nature and which represent 11Aliivibrio,Photobacterium, andVibriospecies, were screened for incongruence of phylogenies based on a representative housekeeping gene (gyrBorpyrH) and a representativeluxgene (luxA). Strains exhibiting incongruence were then subjected to detailed phylogenetic analysis of horizontal transfer by using multiple housekeeping genes (gyrB,recA, andpyrH) and multipleluxgenes (luxCDABEG). In nearly all cases, housekeeping gene andluxgene phylogenies were congruent, and there was no instance in which theluxgenes of one luminous species had replaced theluxgenes of another luminous species. Therefore, theluxgenes are predominantly vertically inherited inVibrionaceae. The few exceptions to this pattern of congruence were as follows: (i) theluxgenes of the only known luminous strain ofVibrio vulnificus, VVL1 (ATCC 43382), were evolutionarily closely related to theluxgenes ofVibrio harveyi; (ii) theluxgenes of two luminous strains ofVibrio chagasii, 21N-12 and SB-52, were closely related to those ofV. harveyiandVibrio splendidus, respectively; (iii) theluxgenes of a luminous strain ofPhotobacterium damselae, BT-6, were closely related to theluxgenes of thelux-rib2operon ofPhotobacterium leiognathi; and (iv) a strain of the luminous bacteriumPhotobacterium mandapamensiswas found to be merodiploid for theluxgenes, and the second set ofluxgenes was closely related to theluxgenes of thelux-rib2operon ofP. leiognathi. In none of these cases of apparent HGT, however, did acquisition of theluxgenes correlate with phylogenetic divergence of the recipient strain from other members of its species. The results indicate that horizontal transfer of theluxgenes in nature is rare and that horizontal acquisition of theluxgenes apparently has not contributed to speciation in recipient taxa.