Development of a Quantitative Competitive PCR Assay for Detection and Quantification of Escherichia coli O157:H7 Cells

A quantitative competitive PCR (QC-PCR) assay was developed to detect and quantify Escherichia coli O157:H7 cells. From 10³ to 10⁸ CFU of E. coli O157:H7 cells/ml was quantified in broth or skim milk, and cell densities predicted by QC-PCR were highly related to viable cell counts (r² = 0.99 and 0.93, respectively). QC-PCR has potential for quantitative detection of pathogenic bacteria in foods.     

Effect of stress on the ability of a phlA-based quantitative competitive PCR assay to monitor biocontrol strain Pseudomonas fluorescens CHA0

A quantitative competitive PCR (QC-PCR) assay targeting the phlA gene of Pseudomonas fluorescens CHA0 was developed and tested in vitro. Statistically significant, positive correlations were found between QC-PCR and both CFU and total cell number when studying cells in log or stationary phase. The correlations disappeared when considering stressed cells.     

Development and use of quantitative competitive PCR assays for relative quantifying rumen anaerobic fungal populations in both in vitro and in vivo systems

This paper describes the use of a quantitative competitive polymerase chain reaction (QC-PCR) assay; using PCR primers to the rRNA locus of rumen fungi and a standard-control DNA including design and validation. In order to test the efficiency of this method for quantifying anaerobic rumen fungi, it has been attempted to evaluate this method in in vitro conditions by comparing with an assay based on measuring cell wall chitin. The changes in fungal growth have been studied when they are grown in in vitro on either untreated (US) or sodium hydroxide treated wheat straw (TS). Results showed that rumen fungi growth was significantly higher in treated samples compared with untreated during the 12 d incubation (P < 0.05) and plotting the chitin assay's results against the competitive PCR's showed high positive correlation (R² ≥ 0.87). The low mean values of the coefficients of variance in repeatability in the QC-PCR method against the chitin assay demonstrated more reliability of this new approach. And finally, the efficiency of this method was investigated in in vivo conditions. Samples of rumen fluid were collected from four fistulated Holstein steers which were fed four different diets (basal diet, high starch, high sucrose and starch plus sucrose) in rotation. The results of QC-PCR showed that addition of these non-structural carbohydrates to the basal diets caused a significant decrease in rumen anaerobic fungi biomass. The QC-PCR method appears to be a reliable and can be used for rumen samples.     

Chitinase Genes in Lake Sediments of Ardley Island, Antarctica

A sediment core spanning approximately 1,600 years was collected from a lake on Ardley Island, Antarctica. The sediment core had been greatly influenced by penguin guano. Using molecular methods, the chitinolytic bacterial community along the sediment core was studied over its entire length. Primers targeting conserved sequences of the catalytic domains of family 18 subgroup A chitinases detected group A chitinases from a wide taxonomic range of bacteria. Using quantitative competitive PCR (QC-PCR), chitinase gene copies in each 1-cm section of the whole sediment column were quantified. QC-PCR determination of the chitinase gene copies indicated significant correlation with phosphorus and total organic carbon concentration, suggesting a historical connection between chitinase gene copies and the amount of penguin guano input into the lake sediment. Most of the chitinase genes cloned from the historic sediment core were novel. Analysis of the chitinase gene diversity in selected sediment layers and in the fresh penguin deposits indicated frequent shifts in the chitinolytic bacterial community over time. Sequence analysis of the 16S rRNA genes of chitinolytic bacteria isolated from the lake sediment revealed that the isolates belonged to Janthinobacterium species, Stenotrophomonas species of γ-Proteobacteria, Cytophaga species of the Cytophaga-Flexibacter-Bacteroides group, and Streptomyces and Norcardiopsis species of Actinobacteria. Chitinase gene fragments were cloned and sequenced from these cultivated chitinolytic bacteria. The phylogeny of the chitinase genes obtained from the isolates did not correspond well to that of the isolates, suggesting acquisition via horizontal gene transfer.     

The relationships between quantitative characteristics of stomata and epidermal cells of leaf epidermis

Negative linear correlations were established inMagnolia soulangeana Soul. —Bod. andLigustrum vulgare L. leaves between the frequency and the size (length) of the stomata and between the frequency of the stomata and the area of epidermal cells. Most correlations were statistically significant at theP = 0.01 level. Positive linear correlations were established between the area and the thickness of epidermal cells. These correlations were near to theP = 0.05 level of statistical significance. A high variation coefficient “v%” of the total number of stomata per leaf was found in both plant species.     

Development of a quantitative competitive PCR assay for detection and quantification of Escherichia coli O157:H7 cells.

A quantitative competitive PCR (QC-PCR) assay was developed to detect and quantify Escherichia coli O157:H7 cells. From 10(3) to 10(8) CFU of E. coli O157:H7 cells/ml was quantified in broth or skim milk, and cell densities predicted by QC-PCR were highly related to viable cell counts (r(2) = 0.99 and 0.93, respectively). QC-PCR has potential for quantitative detection of pathogenic bacteria in foods.     

Investigating the expression of pluripotency-related genes in human amniotic fluid cells: A semi-quantitative comparison between different subpopulations,from primary to cultured amniocytes

Various classifications have been proposed for human amniotic subpopulations, including classification of spindle-shaped (SS) and round-shaped (RS) cells, as well as the more referred triple-category of epithelioid (E-type) cells, amniotic fluid-specific (AF-type) cells and fibroblastoid (F-type) cells. The present study aims to investigate these amniotic subpopulations regarding the expression of some stem cell markers, including OCT4, NANOG, SOX2, C-KIT (CD117), C-MYC, KLF4, and THY1 (CD90). Flow cytometry was performed to characterize the isolated clonal subpopulations for a hematopoietic and a mesenchymal marker using PE-CD31 and FITC-CD90, respectively. A semi-quantitative RT-PCR analysis was carried out on the isolates in the second half of their lifespan when the cells were at the stationary phase of the growth curve. Characterization of isolated cells demonstrated that all clones including both epithelioid and fibroblastoid cells, had mesenchymal, not hematopoietic, lineage. RT-PCR analysis also revealed a higher expression of the target genes in epithelioid cells. Furthermore, the expression pattern of the genes and their correlations were remarkably different between primary- and long term-cultured amniocytes. Taken together, our results showed that the primary-cultured cells express the stemness genes equally, whereas the long term-cultured amniocytes exhibited a highly variable manner in the expression pattern of the genes. Diverse derivation site of amniocytes and individual genetic background can potentially explain the observed variation in the expression level of the target genes. These can also explain why amniocytes differ in many respects observed in our study, including survival rate, plastic adhesion, and growth characteristics.     

Nitric oxide releasing acridone carboxamide derivatives as reverters of doxorubicin resistance in MCF7/Dx cancer cells

A series of nitric oxide donating acridone derivatives are synthesized and evaluated for in vitro cytotoxic activity against different sensitive and resistant cancer cell lines MCF7/Wt, MCF7/Mr (BCRP overexpression) and MCF7/Dx (P-gp expression). The results showed that NO-donating acridones are potent against both the sensitive and resistant cells. Structure activity relationship indicate that the nitric oxide donating moiety connected through a butyl chain at N¹⁰ position as well as morpholino moiety linkage through an amide bridge on the acridone ring system at C-2 position, are required to exert a good cytotoxic effect. Further, good correlations were observed when cytotoxic properties were compared with in vitro nitric oxide release rate, nitric oxide donating group potentiated the cytotoxic effect of the acridone derivatives. Exogenous release of nitric oxide by NO donating acridones enhanced the accumulation of doxorubicin in MCF7/Dx cell lines when it was coadministered with doxorubicin, which inhibited the efflux process of doxorubicin. In summary, a nitric oxide donating group can potentiate the anti-MDR property of acridones.     

石家庄市空气花粉散布规律及与气候因子的关系

石家庄市2007—2009连续两年空气花粉分析表明:受植物花期影响,春季以木本植物花粉为主,夏、秋季以草本植物花粉为主,不同类型花粉通量存在一定年际差异。松属、杨属、胡桃属等当地花粉含量占花粉组合的80.0%以上,桦木属、栎属、虎榛子属等区域花粉含量低于20.0%,显示空气花粉能较好地反映周围植被,但也受区域植被的影响。依据空气花粉通量变化规律,石家庄市主要空气花粉类型通量从高到低排在前5位的依次为:胡桃属、悬铃木属、蒿属、杨属、藜科,均为高致敏类型,花粉过敏症患者在其花期或通量较高时期应早作防范。空气花粉百分含量与气候因子之间的(CCA)分析结果显示,其主要受风速与水汽压影响;不同季节主要花粉类型通量与气候因子的相关分析表明:春季和秋季空气花粉通量主要受气温和水汽压的影响,夏季主要受相对湿度和水汽压的影响,冬季与气候因子相关较弱。     

Evaluation of a Rapid, Quantitative Real-Time PCR Method for Enumeration of Pathogenic Candida Cells in Water

Quantitative PCR (QPCR) technology, incorporating fluorigenic 5′ nuclease (TaqMan) chemistry, was utilized for the specific detection and quantification of six pathogenic species of Candida (C. albicans, C. tropicalis, C. krusei, C. parapsilosis, C. glabrata and C. lusitaniae) in water. Known numbers of target cells were added to distilled and tap water samples, filtered, and disrupted directly on the membranes for recovery of DNA for QPCR analysis. The assay's sensitivities were between one and three cells per filter. The accuracy of the cell estimates was between 50 and 200% of their true value (95% confidence level). In similar tests with surface water samples, the presence of PCR inhibitory compounds necessitated further purification and/or dilution of the DNA extracts, with resultant reductions in sensitivity but generally not in quantitative accuracy. Analyses of a series of freshwater samples collected from a recreational beach showed positive correlations between the QPCR results and colony counts of the corresponding target species. Positive correlations were also seen between the cell quantities of the target Candida species detected in these analyses and colony counts of Enterococcus organisms. With a combined sample processing and analysis time of less than 4 h, this method shows great promise as a tool for rapidly assessing potential exposures to waterborne pathogenic Candida species from drinking and recreational waters and may have applications in the detection of fecal pollution.     

Changes in the flocking behaviour of wintering English titmice with time,weather and supplementary food

Over the course of one winter, the food supply of birds living in a deciduous woodland in southern England was supplemented and unsupplemented during alternating periods. In the presence of substantial predation pressure from hawks, the sociality of blue tits, Parus caeruleus, and great tits, P. major, showed significant partial correlations with several weather and temporal factors when the woodland was unsupplemented. Such correlations between social behaviour and abiotic factors diminished significantly when the birds had access to extra food. Blue tits and great tits without access to supplemental food flocked significantly more often with other species while foraging than when they were food-supplemented. Long-tailed tits, Aegithalos caudatus, ignored the artificial food and foraged in mixed-species flocks to the same extent in both unsupplemented and food-supplemented periods. Results disprove the hypothesis that mixed-species foraging groups are caused by increased predation protection alone, and they support the hypotheses that mixed-species foraging groups are caused by increased foraging efficiency alone or by a combination of increased foraging efficiency and increased protection from predators.     

Genetic correlations of fighting ability with somatic cells and longevity in cattle

The success in competitions may be stressful for animals and costly in terms of immune functions and longevity. Focusing on Aosta Chestnut and Aosta Black Pied cattle, selected for their fighting ability in traditional competitions, this study investigated the genetic relationships of fighting ability with udder health traits (somatic cell score and two threshold traits for somatic cells), longevity (length of productive life and number of calvings) and test-day milk, fat and protein yield. Herdbook information and phenotypic records that have been routinely collected for breeding programs in 16 years were used for the abovementioned traits. Data belonged to 9328 cows and 19 283 animals in pedigree. Single-trait animal model analyses were run using a Gibbs sampling algorithm to estimate the variance components of traits, and bivariate analyses were then performed to estimate the genetic correlations. Moderate positive genetic correlations (r_a) were found for fighting ability with somatic cell score (r_a=0.255), suggesting that greater fighting ability is genetically related to a detriment in udder health, in agreement with the theory. The high positive genetic correlation between fighting ability and longevity (average r_a=0.669) suggests that the economic importance of fighting ability (the winning cows get an higher price at selling) had probably masked the true genetic covariances. The genetic correlation between milk yield traits and fighting ability showed large intervals, but the negative values (average r_a=−0.121) agreed with previous research. This study is one of the few empirical studies on genetic correlations for the competitive success v. immune functions and longevity traits. The knowledge of the genetic correlations among productive and functional traits of interest, including fighting ability, is important in animal breeding for a sustainable genetic improvement.     

Leaf anatomy is not correlated to CAM function in a C3+CAM hybrid species,Yucca gloriosa

Background and AimsCrassulacean acid metabolism (CAM) is often considered to be a complex trait, requiring orchestration of leaf anatomy and physiology for optimal performance. However, the observation of trait correlations is based largely on comparisons between C₃ and strong CAM species, resulting in a lack of understanding as to how such traits evolve and the level of intraspecific variability for CAM and associated traits.MethodsTo understand intraspecific variation for traits underlying CAM and how these traits might assemble over evolutionary time, we conducted detailed time course physiological screens and measured aspects of leaf anatomy in 24 genotypes of a C₃+CAM hybrid species, Yucca gloriosa (Asparagaceae). Comparisons were made to Y. gloriosa’s progenitor species, Y. filamentosa (C₃) and Y. aloifolia (CAM).Key ResultsBased on gas exchange and measurement of leaf acids, Y. gloriosa appears to use both C₃ and CAM, and varies across genotypes in the degree to which CAM can be upregulated under drought stress. While correlations between leaf anatomy and physiology exist when testing across all three Yucca species, such correlations break down at the species level in Y. gloriosa.ConclusionsThe variation in CAM upregulation in Y. gloriosa is a result of its relatively recent hybrid origin. The lack of trait correlations between anatomy and physiology within Y. gloriosa indicate that the evolution of CAM, at least initially, can proceed through a wide combination of anatomical traits, and more favourable combinations are eventually selected for in strong CAM plants.     

Effects of surrounding landscape on parasitism of alfalfa aphids in an IPM crop system in northern Catalonia

The parasitism (Hymenoptera, Braconidae, Aphidiinae) of alfalfa aphids (Hemiptera, Aphididae) was determined during three crop growing seasons. The highest rates of parasitism of Acyrthosiphon pisum Harris and of Therioaphis trifolii Monell occurred during the first-second and the fourth alfalfa intercuts, respectively. The landscape surrounding the fields affected only parasitism rates of A. pisum. During the second intercut the forest area had a negative influence on parasitism rates, whereas the bordering surfaces of alfalfa and winter cereals had a positive influence. Positive correlations were found between the rates of parasitism of A. pisum and the rate of aphid population increase in the first intercut. By contrast, negative correlations were found in the second intercut, when the aphid population peaked, suggesting that parasitoids contribute to the regulation of the aphid. This study stresses that regulation of alfalfa aphids cannot be explained solely on the basis of one functional group of natural enemies.     

Estimates of heritability and genetic correlations for milk coagulation properties and individual laboratory cheese yield in Sarda ewes

Objective of this study was to estimate genetic parameters of milk coagulation properties (MCPs) and individual laboratory cheese yield (ILCY) in a sample of 1018 Sarda breed ewes farmed in 47 flocks. Rennet coagulation time (RCT), curd-firming time (k₂₀) and curd firmness (a₃₀) were measured using Formagraph instrument, whereas ILCY were determined by a micromanufacturing protocol. About 10% of the milk samples did not coagulate within 30 min and 13% had zero value for k₂₀. The average ILCY was 36%. (Co)variance components of considered traits were estimated by fitting both single- and multiple-trait animal models. Flock-test date explained from 13% to 28% of the phenotypic variance for MCPs and 26% for ILCY, respectively. The largest value of heritability was estimated for RCT (0.23±0.10), whereas it was about 0.15 for the other traits. Negative genetic correlations between RCT and a₃₀ (−0.80±0.12), a₃₀ and k₂₀ (−0.91±0.09), and a₃₀ and ILCY (−0.67±0.08) were observed. Interesting genetic correlations between MCPs and milk composition (r_G>0.40) were estimated for pH, NaCl and casein. Results of the present study suggest to use only one out of three MCPs to measure milk renneting ability, due to high genetic correlations among them. Moreover, negative correlations between ILCY and MCPs suggest that great care should be taken when using these methods to estimate cheese yield from small milk samples.     

Quantification of viable Legionella pneumophila cells using propidium monoazide combined with quantitative PCR

One of the greatest challenges of implementing fast molecular detection methods as part of Legionella surveillance systems is to limit detection to live cells. In this work, a protocol for sample treatment with propidium monoazide (PMA) in combination with quantitative PCR (qPCR) has been optimized and validated for L. pneumophila as an alternative of the currently used time-consuming culture method. Results from PMA-qPCR were compared with culture isolation and traditional qPCR. Under the conditions used, sample treatment with 50 μM PMA followed by 5 min of light exposure were assumed optimal resulting in an average reduction of 4.45 log units of the qPCR signal from heat-killed cells. When applied to environmental samples (including water from cooling water towers, hospitals, spas, hot water systems in hotels, and tap water), different degrees of correlations between the three methods were obtained which might be explained by different matrix properties, but also varying degrees of non-culturable cells. It was furthermore shown that PMA displayed substantially lower cytotoxicity with Legionella than the alternative dye ethidium monoazide (EMA) when exposing live cells to the dye followed by plate counting. This result confirmed the findings with other species that PMA is less membrane-permeant and more selective for the intact cells. In conclusion, PMA-qPCR is a promising technique for limiting detection to intact cells and makes Legionella surveillance data substantially more relevant in comparison with qPCR alone. For future research it would be desirable to increase the method's capacity to exclude signals from dead cells in difficult matrices or samples containing high numbers of dead cells.     

Litter production and seasonality of mangroves in Papua New Guinea

Productivity, as measured by litter trapping, of a mangrove dominated by Rhizophora stylosa Griff. at Motupore Island (lat. 9° 31′34′?S; long. 147° 17$\text{\$}\text{?}$02‘ E) was 1430 g dry weight m^?2 year^?1. This is a high figure when compared with other studied mangrove sites. Phenological data were obtained for R. stylosa, R. apiculata Blume and Sonneratia alba Smith. All species have a major leaf fall in the wet season. Flowering in both Rhizophora species is greatest during the wet season, but S. alba peaks during the dry season. Leaf emergence data were only available for R. stylosa and these appeared to be trimodal. Correlations were calculated for each component with rainfall, wind run, maximum temperature and minimum temperature. Some significant correlations were obtained with rainfall and maximum temperature. These correlations are discussed and it is suggested that the seasonality of mangrove phenologies needs to be considered in terms of whole tree physiology rather than isolated environmental factors.