bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA copy number changes in high-grade malignant peripheral nerve sheath tumors by array CGH
Authors: Kresse Stine H , Skårn Magne , Ohnstad Hege O , Namløs Heidi M , Bjerkehagen Bodil , Myklebost Ola , Meza-Zepeda Leonardo A 
Published: June 2008

Abstract

Background
Malignant peripheral nerve sheath tumors (MPNSTs) are rare and highly aggressive soft tissue tumors showing complex chromosomal aberrations. In order to identify recurrent chromosomal regions of gain and loss, and thereby novel gene targets of potential importance for MPNST development and/or progression, we have analyzed DNA copy number changes in seven high-grade MPNSTs using microarray-based comparative genomic hybridization (array CGH).

Results
Considerable more gains than losses were observed, and the most frequent minimal recurrent regions of gain included 1q24.1-q24.2, 1q24.3-q25.1, 8p23.1-p12, 9q34.11-q34.13 and 17q23.2-q25.3, all gained in five of seven samples. The 17q23.2-q25.3 region was gained in all five patients with poor outcome and not in the two patients with disease-free survival. cDNA microarray analysis and quantitative real-time reverse transcription PCR were used to investigate expression of genes located within these regions. The gene lysyl oxidase-like 2 (LOXL2) was identified as a candidate target for the 8p23.1-p12 gain. Within 17q, the genes topoisomerase II-α (TOP2A), ets variant gene 4 (E1A enhancer binding protein, E1AF) (ETV4) and baculoviral IAP repeat-containing 5 (survivin) (BIRC5) showed increased expression in all samples compared to two benign tumors. Increased expression of these genes has previously been associated with poor survival in other malignancies, and for TOP2A, in MPNSTs as well. In addition, we have analyzed the expression of five micro RNAs located within the 17q23.2-q25.3 region, but none of them showed high expression levels compared to the benign tumors.

Conclusion
Our study shows the potential of using DNA copy number changes obtained by array CGH to predict the prognosis of MPNST patients. Although no clear correlations between the expression level and patient outcome were observed, the genes TOP2A, ETV4 and BIRC5 are interesting candidate targets for the 17q gain associated with poor survival.
A plastome primer set for comprehensive quantitative real time RT-PCR analysis of Zea mays: a starter primer set for other Poaceae species
Authors: Sharpe Richard M , Dunn Sade N , Cahoon A Bruce 
Published: June 2008

Abstract

Background
Quantitative Real Time RT-PCR (q2(RT)PCR) is a maturing technique which gives researchers the ability to quantify and compare very small amounts of nucleic acids. Primer design and optimization is an essential yet time consuming aspect of using q2(RT)PCR. In this paper we describe the design and empirical optimization of primers to amplify and quantify plastid RNAs from Zea mays that are robust enough to use with other closely related species.

Results
Primers were designed and successfully optimized for 57 of the 104 reported genes in the maize plastome plus two nuclear genes. All 59 primer pairs produced single amplicons after end-point reverse transcriptase polymerase chain reactions (RT-PCR) as visualized on agarose gels and subsequently verified by q2(RT)PCR. Primer pairs were divided into several categories based on the optimization requirements or the uniqueness of the target gene. An in silico test suggested the majority of the primer sets should work with other members of the Poaceae family. An in vitro test of the primer set on two unsequenced species (Panicum virgatum and Miscanthus sinensis) supported this assumption by successfully producing single amplicons for each primer pair.

Conclusion
Due to the highly conserved chloroplast genome in plant families it is possible to utilize primer pairs designed against one genomic sequence to detect the presence and abundance of plastid genes or transcripts from genomes that have yet to be sequenced. Analysis of steady state transcription of vital system genes is a necessary requirement to comprehensively elucidate gene expression in any organism. The primer pairs reported in this paper were designed for q2(RT)PCR of maize chloroplast genes but should be useful for other members of the Poaceae family. Both in silico and in vitro data are presented to support this assumption.
The moose throat bot fly Cephenemyia ulrichii larvae (Diptera: Oestridae) found developing in roe deer (Capreolus capreolus) for the first time
Authors: Nilssen Arne C , Isomursu Marja , Oksanen Antti 
Published: June 2008

AbstractAbout fifty larvae of Cephenemyia ulrichii Brauer (Diptera: Oestridae), some of them nearly full-grown third instars, were found in the throat of a roe deer (Capreolus capreolus) in June 2007 near Helsinki in Finland. The parasite is considered to be host specific, occurring only in the moose (Alces alces), and this paper is apparently the first report of a successful infestation in an aberrant host.
Exogenous nitric oxide requires an endothelial glycocalyx to prevent postischemic coronary vascular leak in guinea pig hearts
Authors: Bruegger Dirk , Rehm Markus , Jacob Matthias , Chappell Daniel , Stoeckelhuber Mechthild , Welsch Ulrich , Conzen Peter , Becker Bernhard F 
Published: June 2008

Abstract
Introduction
Postischemic injury to the coronary vascular endothelium, in particular to the endothelial glycocalyx, may provoke fluid extravasation. Shedding of the glycocalyx is triggered by redox stress encountered during reperfusion and should be alleviated by the radical scavenger nitric oxide (NO). The objective of this study was to investigate the effect of exogenous administration of NO during reperfusion on both coronary endothelial glycocalyx and vascular integrity.

Methods
Isolated guinea pig hearts were subjected to 15 minutes of warm global ischemia followed by 20 minutes of reperfusion in the absence (Control group) and presence (NO group) of 4 μM NO. In further experiments, the endothelial glycocalyx was enzymatically degraded by means of heparinase followed by reperfusion without (HEP group) and with NO (HEP+NO group).

Results
Ischemia and reperfusion severely damaged the endothelial glycocalyx. Shedding of heparan sulfate and damage assessed by electron microscopy were less in the presence of NO. Compared with baseline, coronary fluid extravasation increased after ischemia in the Control, HEP, and HEP+NO groups but remained almost unchanged in the NO group. Tissue edema was significantly attenuated in this group. Coronary vascular resistance rose by 25% to 30% during reperfusion, but not when NO was applied, irrespective of the state of the glycocalyx. Acute postischemic myocardial release of lactate was comparable in the four groups, whereas release of adenine nucleotide catabolites was reduced 42% by NO. The coronary venous level of uric acid, a potent antioxidant and scavenger of peroxynitrite, paradoxically decreased during postischemic infusion of NO.

Conclusion
The cardioprotective effect of NO in postischemic reperfusion includes prevention of coronary vascular leak and interstitial edema and a tendency to forestall both no-reflow and degradation of the endothelial glycocalyx.
Inhibition of casein kinase 1-epsilon induces cancer-cell-selective, PERIOD2-dependent growth arrest
Authors: Yang Wan Seok , Stockwell Brent R 
Published: June 2008

Abstract
Background
Kinases are under extensive investigation as targets for drug development. Discovering novel kinases whose inhibition induces cancer-cell-selective lethality would be of value. Recent advances in RNA interference have enabled the realization of this goal.

Results
We screened 5,760 short hairpin RNA clones targeting the human kinome to detect human kinases on which cancer cells are more dependent than normal cells. We employed a two-step screening strategy using human sarcoma cell lines and human fibroblast-derived isogenic cell lines, and found that short hairpin RNAs targeting CSNK1E, a clock gene that regulates circadian rhythms, can induce selective growth inhibition in engineered tumor cells. Analysis of gene-expression data revealed that CSNK1E is overexpressed in several cancer tissue samples examined compared to non-tumorigenic normal tissue, suggesting a positive role of CSNK1E in neogenesis or maintenance. Treatment with IC261, a kinase domain inhibitor of casein kinase 1-epsilon (CK1ε), a protein product of CSNK1E, showed a similar degree of cancer-cell-selective growth inhibition. In a search for substrates of CK1ε that mediate IC261-induced growth inhibition, we discovered that knocking down PER2, another clock gene involved in circadian rhythm control, rescues IC261-induced growth inhibition.

Conclusion
We identified CK1ε as a potential target for developing anticancer reagents with a high therapeutic index. These data support the hypothesis that circadian clock genes can control the cell cycle and cell survival signaling, and emphasize a central role of CK1ε and PERIOD2 in linking these systems.
Pulmonary eosinophilia requires interleukin-5, eotaxin-1, and CD4+ T cells in mice immunized with respiratory syncytial virus G glycoprotein
Authors: Johnson Teresa R , Rothenberg Marc E , Graham Barney S 
Published: June 2008

AbstractSevere illness, type 2 cytokine production, and pulmonary eosinophilia are adverse immune responses resulting from respiratory syncytial virus (RSV) challenge of vvGs-immunized mice. We have shown IL-4 and IL-13 activity must be simultaneously inhibited to reduce disease severity. We now address the contributions of IL-5, eotaxin-1, and CD4+ and CD8+ T cells to the induction of disease-enhancing immune responses. Depletion of CD4+ T cells during immunization prevented IL-4, IL-13, and eotaxin-1 production, diminished eosinophilia, and reduced weight loss. Conversely, CD8+ T cell depletion did not decrease eosinophilia, weight loss, or type 2 cytokines but did dramatically reduce mucus production and increase eotaxin production. Anti-IL-5 administration at immunization or challenge significantly decreased pulmonary eosinophilia. Strikingly, there were not concomitant decreases in weight loss. Following RSV challenge eotaxin-1-deficient mice immunized with vvGs exhibited significantly less eosinophilia without decreased weight loss or type 2 cytokine production. We conclude CD4+ T cell production of IL-5 and induction of eotaxin-1 are required for vvGs-induced eosinophilia following RSV challenge, while CD8+ T cells appear to down-regulate eotaxin-1 and mucus production. In summary, we demonstrate that pulmonary eosinophilia 1) is a by-product of memory CD4+ T cell activation, 2) does not necessarily correlate with mucus production, and, most importantly, 3) is not required for the RSV G-induced illness in mice. These findings have important implications for the evaluation of candidate RSV vaccines.
CCR7 regulates B16 murine melanoma cell tumorigenesis in skin
Authors: Fang Lei , Lee Vivian C , Cha Emily , Zhang Hong , Hwang Sam T 
Published: June 2008

AbstractTumor cell-associated chemokine receptors play distinct roles in cancer biology, including enhancement of lymph node (LN) metastasis. To determine if CCR7 influences tumor formation in skin, we inoculated B16 cells transduced with CCR7 and luciferase (CCR7-luc-B16) or with retroviral vector and luciferase (pLNCX2-luc-B16) into ear skin and footpads of wild-type (WT) mice. In contrast to pLNCX2-luc-B16 cells, 97% of CCR7-luc-B16 cell-inoculated mice formed skin tumors as well as cervical LN metastases by Day 21 following ear inoculation. CCR7-expressing and control B16 cells, however, formed tumors of similar size and with high-efficiency in SCID-beige mice. Cells from both lines accumulated in the skin of WT mice in similar numbers until Day 7. By Day 11, however, control cells decreased tenfold, whereas CCR7-luc-B16 cells formed small tumor nodules. Tumor cells were infrequently detected in draining cervical LNs up to 11 days after injection of both cell lines, but stable nodal metastases were only observed after CCR7-luc-B16 ear tumors had been established (∼Day 21). ELISPOT assays revealed that IFN-γ-producing cells in draining LNs from CCR7-luc-B16-injected ears were reduced through Day 7. After footpad injection, tumor formation by CCR7-expressing B16 cells was enhanced only with small, initial tumor cell inocula. With larger inocula, tumor formation was equivalent, but the numbers of tumor-infiltrating leukocytes were reduced by approximately sixfold in CCR7-B16 tumors compared with pLNCX2-B16 tumors of equal size. IFN-γ and CXCL10 were reduced 35- and sixfold, respectively, in CCR7-B16 cell tumors (vs. control tumors). Thus, CCR7 expression enhances tumorigenesis in addition to facilitating LN metastasis.
Experimental and numerical study to predict crack growth in a thick-walled cylinder under fatigue loading
Authors: Malik M A , Salam I , Abid M 
Published: June 2008

Experimental and numerical studies were carried out to predict the crack growth rate under fatigue loading in a thick-walled cylinder made of aluminum alloy. Extensive experimental fatigue-crack growth data on middle tension samples was compiled and applied to simulate and predict the crack growth process using detailed two-dimensional parametric finite-element (FE) technique. The fatigue-crack propagation was simulated, based on linear elastic fracture mechanics and stress intensity factor determination. The FE model provided results of crack-growth analysis optimized for stress levels ranging from 40 per cent to 25 per cent of the material yield stress. Fatigue-life analysis of the samples showed that the results obtained from the two techniques were in good agreement up to a stress range of 79 MPa. However, at lower stress ranges, the number of cycles to failure as determined by FE analysis (FEA) was smaller than found experimentally. The experimental results were 13 per cent and 36 per cent higher than FEA results at stress ranges of 63 and 49 MPa, respectively. This disparity was explained in terms of the crack growth rates near the threshold stress intensity factor range.
Acute toxicity of acidity in larvae and adults of four stream salamander species (Plethodontidae)
Authors: Green Linda E , Peloquin Jennifer E 
Published: June 2008

Abstract
High levels of acid deposition have severely affected streamwater chemistry in the southern Appalachians. Plethodontid stream salamanders living in and around headwater streams rely on cutaneous respiration and are highly susceptible to changes in water quality. We examined the sensitivity to low pH conditions in four stream salamanders by monitoring the response to six pH treatments ranging from pH 2.75 to 6.5. To quantify acid tolerance, we determined median lethal concentrations (LC50) in 96-h laboratory bioassays. This is the first study to quantify the level of sensitivity of stream salamanders to acidic conditions, indicating that stream salamanders are acid tolerant compared with many other lotic organisms. We found that acid tolerance is a species-specific trait with intraspecific variation shaped by life stage and body size. Mortality occurred at pH levels less than 4.2. The acid sensitivity of Desmognathus quadramaculatus larvae (LC50 = pH 3.95) was highest compared to sensitivity of Eurycea cirrigera larvae (LC50 = 3.6), Gyrinophilus porphyriticus larvae (LC50 = 3.5), and Pseudotriton ruber larvae (LC50 = 3.5). Larval survival was lower than adult survival in low pH treatments for E. cirrigera (adult LC50 = 3.1) and D. quadramaculatus (adult LC50 = 3.5). Salamanders responded to sublethal exposure to acidity with lethargic movements and decreased swimming speed. These results suggest that episodic acid events that cause streamwater pH to drop near 4.2 may cause mortality or induce sublethal effects, such as slower swimming speed. Because salamander larvae are more sensitive to acidic conditions than adults, we recommend that population monitoring programs extend methodology to include reliable estimates of larval population sizes.
Enzyme-linked immunosorbent assay for screening dioxin soil contamination by uncontrolled combustion during informal recycling in slums
Authors: Trindade Mirta , Nording Malin , Nichkova Mikaela , Spinnel Erik , Haglund Peter , Last Michael S , Gee Shirley , Hammock Bruce , Last Jerold A , González-Sapienza Gualberto , Brena Beatriz M 
Published: June 2008

Abstract
Uncontrolled combustion due to garbage recycling is a widespread activity among slum dwellers in distressed economy countries and has been indicated as a major source of dioxin contamination. However, because of the high cost and complexity of gas chromatography/high-resolution mass spectrometry (GC-HRMS) analysis, the magnitude of the problem remains largely unknown. The present study describes a first approach toward the use of a dioxin antibody-based enzyme-linked immunosorbent assay (ELISA) as the basis for a sustainable, simple, and low-cost monitoring program to assess the toxicological impact of uncontrolled combustion in slums. A panel of 16 samples was analyzed by GC-HRMS and ELISA on split extracts. Close to 20% of the analyzed samples showed dioxin concentrations up to almost twice the guidance level for residential soil in several countries, pointing out the need for performing a large-scale monitoring program. Despite the potential for variations in dioxin congener distribution due to the mixed nature of the incinerated material, there was a good correlation between the toxic equivalents as determined by GC-HRMS and ELISA. Furthermore, an interlaboratory ELISA validation showed that the capacity to perform the dioxin ELISA was successfully transferred between laboratories. It was concluded that the ELISA method performed very well as a screening tool to prioritize samples for instrumental analysis, which allows cutting down costs significantly.
Epoxiconazole causes changes in testicular histology and sperm production in the Japanese quail (Coturnix coturnix japonica)
Authors: Grote Konstanze , Niemann Lars , Selzsam Britta , Haider Wolfgang , Gericke Christine , Herzler Matthias , Chahoud Ibrahim 
Published: June 2008

Abstract
The fungicide epoxiconazole (Epox), a triazole, belongs to the group of azole compounds that are extensively used as fungicides in various fruit crops. The frequent use of agricultural lands for wintering by migrating birds can be the source of their increased dietary intake of agricultural pesticides. We investigated whether exposure to Epox causes effects on avian fertility and reproduction, using the Japanese quail (Coturnix coturnix japonica) as a model species for the assessment of reproductive effects of pesticides in wild birds. Epox was administered to adult Japanese quail for three weeks at dietary levels of 10, 50, and 500 ppm, and possible effects on reproduction were investigated. Epox administration resulted in a significantly decreased number of spermatids in the 50- and 500-ppm dose groups. Histopathology showed a reduced number of testicular canaliculi with visible germ cells and a reduction in spermatid number. However, testis weight was not affected up to the highest dose level. No impact was observed on hormone levels, fertility, and reproductive outcome, as laying rate and percentage of fertile eggs were not altered. Likewise, treatment had no influence on the egg or chick parameters evaluated. A time- and dose-related transfer of Epox into the eggs was determined in all treatment groups. We conclude that dietary treatment of Japanese quail with 50 and 500 ppm of the triazole fungicide Epox resulted in a clear impact on the testis. The evaluation of the additional endpoints spermatid count and testicular histology have proven useful and are recommended for future studies on avian reproduction.
A database of fish biotransformation rates for organic chemicals
Authors: Arnot Jon A , Mackay Don , Parkerton Thomas F , Bonnell Mark 
Published: June 2008

Abstract
Biotransformation is a key process that can mitigate the bioaccumulation potential of organic substances and is an important parameter for exposure assessments. A recently published method for estimating whole-body in vivo metabolic biotransformation rate constants (kM) is applied to a database of measured laboratory bioconcentration factors and total elimination rate constants for fish. The method uses a kinetic mass balance model to estimate rates of chemical uptake and elimination when measured values are not reported. More than 5,400 measurements for more than 1,000 organic chemicals were critically reviewed to compile a database of 1,535 kM estimates for 702 organic chemicals. Biotransformation rates range over six orders of magnitude across a diverse domain of chemical classes and structures. Screening-level uncertainty analyses provide guidance for the selection and interpretation of kM values. In general, variation in kM estimates from different routes of exposure (water vs diet) and between fish species is approximately equal to the calculation uncertainty in kM values. Examples are presented of structure–biotransformation relationships. Biotransformation rate estimates in the database are compared with estimates of biodegradation rates from existing quantitative structure–activity relationship models. Modest correlations are found, suggesting some consistency in biotransformation capabilities between fish and microorganisms. Additional analyses to further explore possible quantitative structure–biotransformation relationships for estimating kM from chemical structure are encouraged, and recommendations for improving the database are provided.
Selection and identification of bacterial strains with methyl-tert-butyl ether, ethyl-tert-butyl ether, and tert-amyl methyl ether degrading capacities
Authors: Purswani Jessica , Pozo Clementina , Rodríguez-Díaz Marina , González-López Jesús 
Published: June 2008

Abstract
Nine bacterial strains isolated from two hydrocarbon-contaminated soils were selected because of their capacity for growth in culture media amended with 200 mg/L of one of the following gasoline oxygenates: Methyl-tert-butyl ether (MTBE), ethyl-tert-butyl ether (ETBE), and tert-amyl methyl ether (TAME). These strains were identified by amplification of their 16S rRNA gene, using fD1 and rD1 primers, and were tested for their capacity to grow and biotransform these oxygenates in both mineral and cometabolic media. The isolates were classified as Bacillus simplex, Bacillus drentensis, Arthrobacter sp., Acinetobacter calcoaceticus, Acinetobacter sp., Gordonia amicalis (two strains), Nocardioides sp., and Rhodococcus ruber. Arthrobacter sp. (strain MG) and A. calcoaceticus (strain M10) consumed 100 (cometabolic medium) and 82 mg/L (mineral medium) of oxygenate TAME in 21 d, respectively, under aerobic conditions. Rhodococcus ruber (strain E10) was observed to use MTBE and ETBE as the sole carbon and energy source, whereas G. amicalis (strain T3) used TAME as the sole carbon and energy source for growth. All the bacterial strains transformed oxygenates better in the presence of an alternative carbon source (ethanol) with the exception of A. calcoaceticus (strain M10). The capacity of the selected strains to remove MTBE, ETBE, and TAME looks promising for application in bioremediation technologies.