bluuebunny/crossref_metadata_2025_split huggingface dataset:
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C Incorporation into Signature Fatty Acids as an Assay for Carbon Allocation in Arbuscular Mycorrhiza
Authors: Olsson Pål Axel , van Aarle Ingrid M. , Gavito Mayra E. , Bengtson Per , Bengtsson Göran 
Published: May 2005

ABSTRACT

The ubiquitous arbuscular mycorrhizal fungi consume significant amounts of plant assimilated C, but this C flow has been difficult to quantify. The neutral lipid fatty acid 16:1ω5 is a quantitative signature for most arbuscular mycorrhizal fungi in roots and soil. We measured carbon transfer from four plant species to the arbuscular mycorrhizal fungus
Glomus intraradices
by estimating
13
C enrichment of 16:1ω5 and compared it with
13
C enrichment of total root and mycelial C. Carbon allocation to mycelia was detected within 1 day in monoxenic arbuscular mycorrhizal root cultures labeled with [
13
C]glucose. The
13
C enrichment of neutral lipid fatty acid 16:1ω5 extracted from roots increased from 0.14% 1 day after labeling to 2.2% 7 days after labeling. The colonized roots usually were more enriched for
13
C in the arbuscular mycorrhizal fungal neutral lipid fatty acid 16:1ω5 than for the root specific neutral lipid fatty acid 18:2ω6,9. We labeled plant assimilates by using
13
CO
2
in whole-plant experiments. The extraradical mycelium often was more enriched for
13
C than was the intraradical mycelium, suggesting rapid translocation of carbon to and more active growth by the extraradical mycelium. Since there was a good correlation between
13
C enrichment in neutral lipid fatty acid 16:1ω5 and total
13
C in extraradical mycelia in different systems (
r
2
= 0.94), we propose that the total amount of labeled C in intraradical and extraradical mycelium can be calculated from the
13
C enrichment of 16:1ω5. The method described enables evaluation of C flow from plants to arbuscular mycorrhizal fungi to be made without extraction, purification and identification of fungal mycelia.
Degradation of Azo Dyes by Laccase and Ultrasound Treatment
Authors: Tauber Michael M. , Guebitz Georg M. , Rehorek Astrid 
Published: May 2005

ABSTRACT
The goal of this work was to investigate the decomposition of azo dyes by oxidative methods, such as laccase and ultrasound treatments. Each of these methods has strong and feeble sides. The laccase treatment showed high decolorization rates but cannot degrade all investigated dyes (reactive dyes), and high anionic strength led to enzyme deactivation. Ultrasound treatment can decolorize all tested dyes after 3 h at a high energy input, and prolonged sonication leads to nontoxic ionic species, which was demonstrated by ion chromatography and toxicity assays. For the first time, it was shown that a combination of laccase and ultrasound treatments can have synergistic effects, which was shown by higher degradation rates. Bulk light absorption and ion-pairing high-performance liquid chromatography (IP-HPLC) were used for process monitoring, while with reversed-phase HPLC, a lower number of intermediates than expected by IP-HPLC was found. Liquid chromatography-mass spectrometry indicated that both acid orange dyes lead to a common end product due to laccase treatment. Acid Orange 52 is demethylated by laccase and ultrasound treatment. Further results confirmed that the main effect of ultrasound is based on ˙OH attack on the dye molecules.
Construction of a Cloning System for the Mass Production of a Virus-Binding Protein Specific for Poliovirus Type 1
Authors: Sano Daisuke , Omura Tatsuo 
Published: May 2005

ABSTRACT

In our previous study, virus-binding proteins (VBPs) demonstrating the ability to strongly bind poliovirus type 1 (PV1) were recovered from a bacterial culture derived from activated sludge. The isolated VBPs would be useful as viral adsorbents for water and wastewater treatments. The VBP gene of activated sludge bacteria was isolated, and the cloning system of the VBP was established. The isolation of the VBP gene from DNA libraries for activated sludge bacteria was achieved with the colony hybridization technique. The sequence of the VBP gene consisted of 807 nucleotides encoding 268 amino acids. Fifteen amino acid sequences were retrieved from 2,137,877 sequences by a homology search using the BLAST server at the National Center for Biotechnology Information. The protein encoded in the isolated genome was considered to be a newly discovered protein from activated sludge culture, because any sequences in protein databases were not perfectly matched with the sequence of the VBP. It was confirmed that
Escherichia coli
BL21 transformed by pRSET carrying the isolated VBP gene could extensively produce the VBP clones. Enzyme-linked immunosorbent assay (ELISA) revealed that the VBP clone exhibited the binding ability with intact particles of PV1. The equilibrium binding constant between PV1 and VBP in the ELISA well was estimated to be 2.1 × 10
7
(M
−1
), which also indicated that the VBP clones have a high affinity with the PV1 particle. The VBP cloning system developed in this study would make it possible to produce a mass volume of VBPs and to utilize them as a new material of the specific adsorbent in several technologies, including virus removal, concentration, and detection.
Molecular Identification and Analysis ofBorrelia burgdorferiSensu Lato in Lizards in the Southeastern United States
Authors: Clark Kerry , Hendricks Amanda , Burge David 
Published: May 2005

ABSTRACTLyme borreliosis (LB) group spirochetes, collectively known asBorrelia burgdorferisensu lato, are distributed worldwide. Wild rodents are acknowledged as the most important reservoir hosts.Ixodes scapularisis the primary vector ofB. burgdorferisensu lato in the eastern United States, and in the southeastern United States, the larvae and nymphs mostly parasitize certain species of lizards. The primary aim of the present study was to determine whether wild lizards in the southeastern United States are naturally infected with Lyme borreliae. Blood samples obtained from lizards in Florida and South Carolina were tested for the presence of LB spirochetes primarily by usingB. burgdorferisensu lato-specific PCR assays that amplify portions of the flagellin (flaB), outer surface protein A (ospA), and 66-kDa protein (p66) genes. Attempts to isolate spirochetes from a small number of PCR-positive lizards failed. However, PCR amplification and sequence analysis of partialflaB,ospA, andp66gene fragments confirmed numerous strains ofB. burgdorferisensu lato, includingBorrelia andersonii,Borrelia bissettii, andB. burgdorferisensu stricto, in blood from lizards from both states.B. burgdorferisensu lato DNA was identified in 86 of 160 (54%) lizards representing nine species and six genera. The high infection prevalence and broad distribution of infection among different lizard species at different sites and at different times of the year suggest that LB spirochetes are established in lizards in the southeastern United States.
Rapid Biosensor for Detection of Antibiotic-Selective Growth of
Escherichia coli
Authors: Gfeller Karin Y. , Nugaeva Natalia , Hegner Martin 
Published: May 2005

ABSTRACT

A rapid biosensor for the detection of bacterial growth was developed using micromechanical oscillators coated in common nutritive layers. The change in resonance frequency as a function of the increasing mass on a cantilever array forms the basis of the detection scheme. The calculated mass sensitivity according to the mechanical properties of the cantilever sensor is ∼50 pg/Hz; this mass corresponds to an approximate sensitivity of ∼100
Escherichia coli
cells. The sensor is able to detect active growth of
E. coli
cells within 1 h. The starting number of
E. coli
cells initially attached to the sensor cantilever was, on average, ∼1,000 cells. Furthermore, this method allows the detection of selective growth of
E. coli
within only 2 h by adding antibiotics to the nutritive layers. The growth of
E. coli
was confirmed by scanning electron microscopy. This new sensing method for the detection of selective bacterial growth allows future applications in, e.g., rapid antibiotic susceptibility testing.
Differential Gene Expression Profiling of
Staphylococcus aureus
Cultivated under Biofilm and Planktonic Conditions
Authors: Resch Alexandra , Rosenstein Ralf , Nerz Christiane , Götz Friedrich 
Published: May 2005

ABSTRACT

It
is well known that biofilm formation by pathogenic staphylococci on
implanted medical devices leads to “chronic polymer-associated
infections.” Bacteria in these biofilms are more resistant to
antibiotics and the immune defense system than their planktonic
counterparts, which suggests that the cells in a biofilm have altered
metabolic activity. To determine which genes are up-regulated in
Staphylococcus aureus
biofilm cells, we carried out a
comparative transcriptome analysis. Biofilm growth was simulated on
dialysis membranes laid on agar plates. Staphylococci were cultivated
planktonically in Erlenmeyer flasks with shaking. mRNA was isolated at
five time points from cells grown under both conditions and used for
hybridization with DNA microarrays. The gene expression patterns of
several gene groups differed under the two growth conditions. In
biofilm cells, the cell envelope appeared to be a very active
compartment since genes encoding binding proteins, proteins involved in
the synthesis of murein and glucosaminoglycan polysaccharide
intercellular adhesin, and other enzymes involved in cell envelope
synthesis and function were significantly up-regulated. In addition,
evidence was obtained that formate fermentation, urease activity, the
response to oxidative stress, and, as a consequence thereof, acid and
ammonium production are up-regulated in a biofilm. These factors might
contribute to survival, persistence, and growth in a biofilm
environment. Interestingly, toxins and proteases were up-regulated
under planktonic growth conditions. Physiological and biochemical tests
for the up-regulation of urease, formate dehydrogenase, proteases, and
the synthesis of staphyloxanthin confirmed the microarray
data.
Use of a Quartz Crystal Microbalance To Investigate the Antiadhesive Potential of
N
-Acetyl-
l
-Cysteine
Authors: Olofsson Ann-Cathrin , Hermansson Malte , Elwing Hans 
Published: May 2005

ABSTRACT

The reduction of bacterial biofilm formation on stainless steel surfaces by
N
-acetyl-
l
-cysteine (NAC) is attributed to effects on bacterial growth and polysaccharide production, as well as an increase in the wettability of steel surfaces. In this report, we show that NAC-coated stainless steel and polystyrene surfaces affect both the initial adhesion of
Bacillus cereus
and
Bacillus subtilis
and the viscoelastic properties of the interaction between the adhered bacteria and the surface. A quartz crystal microbalance with dissipation was shown to be a powerful and sensitive technique for investigating changes in the applied NAC coating for initial cell surface interactions of bacteria. The kinetics of frequency and dissipation shifts were dependent on the bacteria, the life cycle stage of the bacteria, and the surface. We found that exponentially grown cells gave rise to a positive frequency shift as long as their cell surface hydrophobicity was zero. Furthermore, when the characteristics of binding between the cell and the surface for different growth phases were compared, the rigidity increased from exponentially grown cells to starved cells. There was a trend in which an increase in the viscoelastic properties of the interaction, caused by the NAC coating on stainless steel, resulted in a reduction in irreversibly adhered cells. Interestingly, for
B. cereus
that adhered to polystyrene, the viscoelastic properties decreased, while there was a reduction in adhered cells, regardless of the life cycle stage. Altogether, NAC coating on surfaces was often effective and could both decrease the initial adhesion and increase the detachment of adhered cells and spores. The most effective reduction was found for
B. cereus
spores, for which the decrease was caused by a combination of these two parameters.
Transcriptome Analysis of Recombinant Protein Secretion by
Aspergillus nidulans
and the Unfolded-Protein Response In Vivo
Authors: Sims Andrew H. , Gent Manda E. , Lanthaler Karin , Dunn-Coleman Nigel S. , Oliver Stephen G. , Robson Geoffrey D. 
Published: May 2005

ABSTRACT

Filamentous fungi have a high capacity for producing large amounts of secreted proteins, a property that has been exploited for commercial production of recombinant proteins. However, the secretory pathway, which is key to the production of extracellular proteins, is rather poorly characterized in filamentous fungi compared to yeast. We report the effects of recombinant protein secretion on gene expression levels in
Aspergillus nidulans
by directly comparing a bovine chymosin-producing strain with its parental wild-type strain in continuous culture by using expressed sequence tag microarrays. This approach demonstrated more subtle and specific changes in gene expression than those observed when mimicking the effects of protein overproduction by using a secretion blocker. The impact of overexpressing a secreted recombinant protein more closely resembles the unfolded-protein response in vivo.
Enumeration of Respiring
Pseudomonas
spp. in Milk within 6 Hours by Fluorescence In Situ Hybridization following Formazan Reduction
Authors: Kitaguchi Akiko , Yamaguchi Nobuyasu , Nasu Masao 
Published: May 2005

ABSTRACT

Respiring
Pseudomonas
spp. in milk were quantified within 6 h by fluorescence in situ hybridization (FISH) with vital staining. FISH with an oligonucleotide probe based on 16S rRNA sequences was used for the specific detection of
Pseudomonas
spp. at the single cell level. 5-Cyano-2,3-ditolyl tetrazolium chloride (CTC) was used to estimate bacterial respiratory activity. The numbers of respiring
Pseudomonas
cells as determined by FISH with CTC staining (CTC-FISH) were almost the same or higher than the numbers of CFU as determined by the conventional culture method.
Dose Determination for Acute
Salmonella
Infection in Pigs
Authors: Loynachan A. T. , Harris D. L. 
Published: May 2005

ABSTRACT

Pigs were exposed to various levels of
Salmonella enterica
subsp.
enterica
serovar Typhimurium by either intranasal inoculation or by subjecting them to a contaminated environment. More than 10
3
salmonellae were required to induce acute
Salmonella
infection. These results indicate that intervention against acute
Salmonella
infection in lairage may be more readily achieved than previously thought.
The risk of menstrual abnormalities after tubal sterilization: a case control study
Authors: shobeiri Mehri Jafari , AtashKhoii Simin 
Published: May 2005

Abstract
Background
Tubal sterilization is the method of family planning most commonly used. The existence of the post-tubal-ligation syndrome of menstrual abnormalities has been the subject of debate for decades.

Methods
In a cross-sectional study, 112 women with the history of Pomeroy type of tubal ligation achieved by minilaparatomy as the case group and 288 women with no previous tubal ligation as the control group were assessed for menstrual abnormalities.

Results
Menstrual abnormalities were not significantly different between the case and control groups (p = 0.824). The abnormal uterine bleeding frequency differences in two different age groups (30–39 and 40–45 years old) were statistically significant (p = 0.0176).

Conclusion
Tubal sterilization does not cause menstrual irregularities.
Adapting developing country epidemiological assessment techniques to improve the quality of health needs assessments in developed countries
Authors: Smith Susan M , Long Jean , Deady Jillian , O'Keeffe Frances , Handy Deirdre , O'Dowd Tom 
Published: May 2005

Abstract
Background
We were commissioned to carry out three health assessments in urban areas of Dublin in Ireland. We required an epidemiologically robust method that could collect data rapidly and inexpensively. We were dealing with inadequate health information systems, weak planning data and a history of inadequate recipient involvement in health service planning. These problems had also been identified by researchers carrying out health assessments in developing countries. This paper reports our experience of adapting a cluster survey model originally developed by international organisations to assess community health needs and service coverage in developing countries and applying our adapted model to three urban areas in Dublin, Ireland

Methods
We adapted the model to control for socio-economic heterogeneity, to take account of the inadequate population list, to ensure a representative sample and to account for a higher prevalence of degenerative and chronic diseases. We employed formal as well as informal communication methods and adjusted data collection times to maximise participation.

Results
The model we adapted had the capacity to ascertain both health needs and health care delivery needs. The community participated throughout the process and members were trained and employed as data collectors. The assessments have been used by local health boards and non-governmental agencies to plan and deliver better or additional services.

Conclusion
We were able to carry out high quality health needs assessments in urban areas by adapting and applying a developing country health assessment method. Issues arose relating to health needs assessment as part of the planning cycle and the role of participants in the process.
Combined Analysis of Efficacy: The Addition of Bevacizumab to Fluorouracil/Leucovorin Improves Survival for Patients With Metastatic Colorectal Cancer
Authors: Kabbinavar Fairooz F. , Hambleton Julie , Mass Robert D. , Hurwitz Herbert I. , Bergsland Emily , Sarkar Somnath 
Published: May 2005

Purpose Bevacizumab (Avastin; Genentech Inc, South San Francisco, CA), a recombinant, humanized anti–vascular endothelial growth factor monoclonal antibody that inhibits tumor angiogenesis, has demonstrated survival benefit in patients with previously untreated metastatic colorectal cancer when combined with irinotecan/fluourouracil (FU)/leucovorin (LV; IFL). Three randomized clinical studies have evaluated bevacizumab in combination with FU/LV alone. A combined analysis of raw data from these studies was performed to better assess the efficacy of bevacizumab with FU/LV. Patients and Methods The analysis used primary efficacy data from three independent studies, including 241 patients in a combined control group receiving either FU/LV or IFL and 249 patients receiving FU/LV/bevacizumab (5 mg/kg once every 2 weeks). The efficacy data included response rate, progression-free survival, and overall survival. Results The median duration of survival was 17.9 months in the FU/LV/bevacizumab group, compared with 14.6 months in the combined control group, corresponding to a hazard ratio for death of 0.74 (P = .008). The median duration of progression-free survival was 8.8 months in the FU/LV/bevacizumab group, compared with 5.6 months in the combined control group, corresponding to a hazard ratio for disease progression of 0.63 (P ≤ .0001). The addition of bevacizumab also improved the response rate (34.1% v 24.5%; P = .019). Conclusion The addition of bevacizumab to FU/LV provides a statistically significant and clinically relevant benefit to patients with previously untreated metastatic colorectal cancer.
Evidence for Distinct Pathomechanisms in Genetic Subgroups of Chronic Lymphocytic Leukemia Revealed by Quantitative Expression Analysis of Cell Cycle, Activation, and Apoptosis-Associated Genes
Authors: Kienle Dirk L. , Korz Christian , Hosch Beate , Benner Axel , Mertens Daniel , Habermann Annett , Kröber Alexander , Jäger Ulrich , Lichter Peter , Döhner Hartmut , Stilgenbauer Stephan 
Published: May 2005

Purpose In patients with chronic lymphocytic leukemia (CLL), the VH mutation status and genomic aberrations (13q−, +12q, 11q−, 17p−) identify distinct prognostic subgroups. The aim was to elucidate biologic mechanisms through which these genetic markers may exert their pathogenic influence. Patients and Methods Twenty-four genes involved in apoptosis, cell cycle, B-cell activation, and B-cell receptor (BCR) signaling were analyzed by real-time quantitative reverse transcription polymerase chain reaction (RQ-PCR) in 82 CLL cases constituting prototypic genetic CLL subgroups as defined by the VH mutation status and the genomic aberrations 13q−, +12, 11q−, and 17p−. Results The VH mutation subgroups were characterized by a differential expression of the BCR associated genes ZAP70 and PI3K. Among the subgroups defined by genomic aberrations, there was a deregulation of candidate genes from the affected critical genomic regions such as CDK4 (up), ATM (down), and TP53 (down) in the groups +12, 11q−, and 17p−, respectively. Additionally, the genomic subgroups were characterized by a significant deregulation of cell cycle and apoptosis regulators: AKT (up) in 13q, E2F1 (up) in +12, MYC (up) and BCL-2 (down) in 17p−, and CCND3 (down) in 11q− as well as 17p−. The 17p− subgroup showed an additional down-regulation of BCR-associated genes such as SYK and PI3K. Conclusion The characteristic gene expression patterns observed implicate a differential regulation of cell cycle, apoptosis, and BCR signaling in the genetic subgroups illustrating distinct pathomechanisms and are evidence for a gene dosage effect being operative in CLL. These findings link the biologic diversity and clinical heterogeneity of CLL.
Phase I Study of the Safety, Tolerability, Pharmacokinetics, and Pharmacodynamics of PTK787/ZK 222584 Administered Twice Daily in Patients With Advanced Cancer
Authors: Thomas Anne L. , Morgan Bruno , Horsfield Mark A. , Higginson Anthony , Kay Andrea , Lee Lucy , Masson Eric , Puccio-Pick Marie , Laurent Dirk , Steward William P. 
Published: May 2005

Purpose PTK787/ZK 222584 (PTK/ZK) is an oral angiogenesis inhibitor targeting all known vascular endothelial growth factor (VEGF) receptor tyrosine kinases, including VEGFR-1/Flt-1, VEGFR-2/KDR, VEGFR-3/Flt-4, the platelet-derived growth factor receptor tyrosine kinase, and the c-kit protein tyrosine kinase. In this phase I dose-escalating study, PTK/ZK was administered bid to exploit the theoretical advantage of maintaining constant drug levels above a threshold known from preclinical data to interfere with VEGF receptor signaling. Patients and Methods Forty-three patients with advanced cancers received single-agent PTK/ZK at doses of 150 to 1,000 mg orally bid. Assessments for safety and pharmacokinetics were performed. Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) was used as a pharmacodynamic marker of response. Results At 1,000 mg bid, the dose-limiting toxicity of reversible grade 3 lightheadedness was observed. Dose-related grade 3 fatigue and vomiting were observed but these were not dose-limiting. Pharmacokinetic data confirmed that PTK/ZK exposure increased with increasing dose up to 500 mg bid and appeared to plateau at higher doses. A greater than 40% reduction in the DCE-MRI bidirectional transfer constant (Ki) at day 2 predicted for nonprogression of disease. Conclusion The maximum-tolerated oral dose of PTK/ZK is 750 mg orally bid. DCE-MRI and pharmacokinetic data indicate that PTK/ZK ≥ 1,000 mg total daily dose is the biologically active dose.