A Strategy to Identify Probes that Detect a High Degree of Polymorphism in Bread Wheat

Although the genetic linkage map of Triticum tauschil, the D-genome progenitor of wheat its available, its use for linkage analysis of hexaploid wheat chromosome regions is hampered by the lack of polymorphism in wheat. Here we describe a strategy to identity probes that detect a high degree of polymorphism in wheat. The strategy involves the use of DNA probes that detect null alleles. About 16% of the Pstl genomic clones from Triticum tauschil detect null alleles in the species. The probes that detect null alleles reveal high degree of polymorphism among hexaploid wheat cultivars. The probes selected following this strategy are expected to detect null alleles throughout the tribe Triticeae, therefore, reveal high degree of polymorphism.     

IMPROVEMENT OF TRIANGLE TEST DATA BY USE OF INCENTIVES

The objectives of this study were to determine the distribution of the sensory panelists' ability to detect differences and to improve the triangle test by minimizing unnecessary guessing. The triangle test was modified to include the use of economic incentives through which panelists voluntarily revealed their ability to detect differences. Panelists were asked to estimate their ability to detect differences and the probability of identifying the odd sample in a triangle test. They were then organized into three ability groups according to their responses. Double triangle tests, followed by triangle tests with economic incentives, were used to evaluate a cereal product and a beverage. The ability to detect differences was modeled as a probability, and the distribution of panelists was estimated. The economic incentives test was more effective when used with the beverage in which differences were less difficult to detect. We found that the economic incentive test discouraged the panelists from guessing unnecessarily, thus increasing the motivation of the panelists to detect differences, and allowing researchers to determine the distribution of discrimination ability.     

Power of different sampling strategies to detect quantitative trait loci variance effects

Summary Many studies have shown that segregating quantitative trait loci (QTL) can be detected via linkage to genetic markers. Power to detect a QTL effect on the trait mean as a function of the number of individuals genotyped for the marker is increased by selectively genotyping individuals with extreme values for the quantitative trait. Computer simulations were employed to study the effect of various sampling strategies on the statistical power to detect QTL variance effects. If only individuals with extreme phenotypes for the quantitative trait are selected for genotyping, then power to detect a variance effect is less than by random sampling. If 0.2 of the total number of individuals genotyped are selected from the center of the distribution, then power to detect a variance effect is equal to that obtained with random selection. Power to detect a variance effect was maximum when 0.2 to 0.5 of the individuals selected for genotyping were selected from the tails of the distribution and the remainder from the center.     

The prevalence of negative studies with inadequate statistical power: an analysis of the plastic surgery literature.

Studies published in the medical literature often neglect to consider the statistical power needed to detect a meaningful difference between study groups. Small sample sizes tend to produce negative results because of low statistical power. Studies that cannot make conclusive statements about their hypotheses can waste resources, deter further research, and impede advances in clinical treatment. The current study reviewed three of the most frequently read plastic surgery journals from 1976 to 1996 to determine the prevalence of inadequately (<80 percent) powered clinical trials and experimental studies that found no difference (negative studies) in the response variable of interest between comparison groups. The statistical power of 54 negative studies using continuous response variables was calculated to detect a difference of 1 SD (+/-1 SD) in means between the comparative groups. The power of another 57 negative studies with dichotomous response (yes/no) variables was calculated to detect a relative change in proportions of 25 percent and 50 percent from the experimental to the control group. It was found that 85 percent of the studies with continuous response variables had inadequate power to detect the desired mean difference of +/-1 SD. In studies with dichotomous response variables, 98 percent had inadequate power to detect a desired 25 percent relative change in proportions, and 74 percent had inadequate power to detect a desired 50 percent relative change in proportions. These results indicate that many of the studies in the plastic surgery literature lack adequate power to detect a moderate-to-large difference between groups. The lack of power makes the interpretation of the studies with negative findings inconclusive. Proper study design dictates that investigators consider a priori the difference between groups that is of clinical interest, and the sample size per group that is needed to provide adequate statistical power to detect the desired difference.     

METHODS FOR DETECTION AND ESTIMATION OF LINKAGE BETWEEN A MARKER LOCUS AND QUANTITATIVE TRAIT LOCI Ⅰ. USING F_2 FAMILY SUBPOPULATION

Several methods heve been proposed over the years to detect linkage between a marker gene and a quantitative trait locus (QTL). Use of isozymes and restriction fragment length polymorphisms (RFLPs) as genetic markers has encouraged the development of new methods to detect linkage. In the paper authors present three methods to detect linkage and two methods to measure recombination frequency (r). The three methods that detect linkage are fit for the test of one or several QTLs of quantitative trait considered as long as the net gene effect vaIue of all loci belonging to a linkage cluster is greater significantly than zero, irrespective of their linkage relationship among the several QTLs.     

Determining sensitive stages for learning to detect predators in larval bronzed frogs: Importance of alarm cues in learning

Successful survival and reproduction of prey organisms depend on their ability to detect their potential predators accurately and respond effectively with suitable defences. Predator detection can be innate or can be acquired through learning. We studied prey–predator interactions in the larval bronzed frogs (Sylvirana temporalis), which have the innate ability to detect certain predators. We conducted a series of experiments to determine if the larval S. temporalis rely solely on innate predator detection mechanisms or can also learn to use more specific cues such as conspecific alarm cues for the purpose. The results of our study clearly indicate that larval S. temporalis use both innate and learned mechanisms for predator detection. Predator-naïve tadpoles could detect kairomones alone as a potential threat and responded by reducing activity, suggesting an innate predator detection mechanism. Surprisingly, predator-naïve tadpoles failed to detect conspecific alarm cues as a potential threat, but learned to do so through experience. After acquiring the ability to detect conspecific alarm cues, they could associate novel predator cues with conspecific alarm cues. Further, post feeding stages of larval S. temporalis are sensitive for learning to detect conspecific alarm cues to label novel predators.     

Altered formation of DNA replication intermediates in cells growing in different culture conditions

In human melanoma cells one can detect two discrete DNA replication intermediates, 10-kb DNA intermediates and Okakzaki fragments. Both intermediates are seen when cells are rapidly growing in medium supplemented with fetal calf serum. When the medium is supplemented with newborn calf serum, one can detect Okakzaki fragments but not 10-kb DNA intermediates. In contrast we do not detect changes in the replicon sizes in the two media.     

Elevated HGF levels in sera from breast cancer patients detected using a protein microarray ELISA

We developed an ELISA in high-density microarray format to detect hepatocyte growth factor (HGF) in human serum. The microassay can detect HGF at sub-pg/mL concentrations in sample volumes of 100 microL or less. The microassay is also quantitative and was used to detect elevated HGF levels in sera from recurrent breast cancer patients. The microarray format provides the potential for high-throughput quantitation of multiple biomarkers in parallel, as demonstrated with a multiplex analysis of five biomarker proteins.     

Detecting Fat Content of Food from a Distance: Olfactory-Based Fat Discrimination in Humans

The desire to consume high volumes of fat is thought to originate from an evolutionary pressure to hoard calories, and fat is among the few energy sources that we can store over a longer time period. From an ecological perspective, however, it would be beneficial to detect fat from a distance, before ingesting it. Previous results indicate that humans detect high concentrations of fatty acids by their odor. More important though, would be the ability to detect fat content in real food products. In a series of three sequential experiments, using study populations from different cultures, we demonstrated that individuals are able to reliably detect fat content of food via odors alone. Over all three experiments, results clearly demonstrated that humans were able to detect minute differences between milk samples with varying grades of fat, even when embedded within a milk odor. Moreover, we found no relation between this performance and either BMI or dairy consumption, thereby suggesting that this is not a learned ability or dependent on nutritional traits. We argue that our findings that humans can detect the fat content of food via odors may open up new and innovative future paths towards a general reduction in our fat intake, and future studies should focus on determining the components in milk responsible for this effect.     

Improvement of RT-PCR detection of chronic bee paralysis virus (CBPV) required by the description of genomic variability in French CBPV isolates

A new RT-PCR test has been developed to diagnose Chronic bee paralysis virus (CBPV) that is able to detect genetically variable viral isolates. In fact, up to 8.7% divergence between partial nucleotide sequences from viral isolates from French honey bees was highlighted in a preliminary variability study. The previously-described RT-PCR was unable to detect all these viral isolates and RT-PCR diagnosis needed improvement. The new RT-PCR test can detect up to 40% more CBPV isolates.     

Detection of linkage between quantitative trait loci and restriction fragment length polymorphisms using inbred lines

Summary In segregating populations, large numbers of individuals are needed to detect linkage between markers, such as restriction fragment length polymorphisms (RFLPs), and quantitative trait loci (QTL), limiting the potential use of such markers for detecting linkage. Fewer individuals from inbred lines are needed to detect linkage. Simulation data were used to test the utility of two methods to detect linkage: maximum likelihood and comparison of marker genotype means. When there is tight linkage, the two methods have similar power, but when there is loose linkage, maximum likelihood is much more powerful. Once inbred lines have been established, they can be screened rapidly to detect QTL for several traits simultaneously. If there is sufficient coverage of the genome with RFLPs, several QTL for each trait may be detected.     

染料木素对铅诱导的PC12 细胞毒性的抑制效应研究

目的:探讨染料木素对铅诱导的细胞毒性的影响。方法:PC12细胞分为对照组、染铅组、染料木素组以及铅加染料木素组;MTT实验检测细胞活力的改变,流式细胞仪检测细胞凋亡水平的变化,荧光探针检测线粒体形态的改变,Western blot方法检测线粒体融合分裂相关蛋白表达水平的变化。结果:铅可诱导PC12细胞活力的下降以及细胞凋亡率的显著增高,染料木素可抑制铅的这些毒性效应。与此同时,铅可诱导线粒体形态的损伤性改变,线粒体融合减少,分裂增多;而加入染料木素之后,线粒体损伤程度显著下降,线粒体分裂减少,融合增多。此外,线粒体融合相关蛋白Mfn2的水平在铅暴露后显著下降,而线粒体分裂相关蛋白Drp1的水平在铅暴露后显著升高,染料木素干预后均有所恢复。结论:染料木素可抑制铅诱导的PC12细胞毒性,其作用可能与其对线粒体融合分裂过程的干预有关。     

Isoelectric focusing of horse serum esterase isozymes and detection of new phenotypes

A new method for separating the isozymes of horse serum esterase is described. The improved resolution has enabled us to detect several previously undescribed phenotypes. This method has also been used to detect two different apparently 'silent' alleles.     

利用错配碱基产生酶切位点快速检测禽类Mx蛋白基因单核苷酸改变

该方法针对无合适酶切位点的检测位点设计引物,应用于禽类Mx蛋白基因631位氨基酸位点的突变检测,利用错配碱基产生内切酶识别的酶切位点检测SNP,尝试一种操作简便结果可靠的检测单核苷酸多态性并能快速判定631位点氨基酸的方法.实验结果表明,利用这种方法产生的酶切位点能有效地对631位氨基酸位点进行分型,可以快速检测SNP.     

UVPAR: fast detection of functional shifts in duplicate genes

Background  

The imprint of natural selection on gene sequences is often difficult to detect. A plethora of methods have been devised to detect genetic changes due to selective processes. However, many of those methods depend heavily on underlying assumptions regarding the mode of change of DNA sequences and often require sophisticated mathematical treatments that made them computationally slow. The development of fast and effective methods to detect modifications in the selective constraints of genes is therefore of great interest.     

Censusing large mammals in Kibale National Park: evaluation of the intensity of sampling required to determine change

Monitoring programmes are essential for management of large mammal populations because they can detect population change. It is vital that we have the means to evaluate the effectiveness of protected areas. Kibale National Park is a stronghold for large mammal conservation in Uganda. Past wildlife surveys in Kibale focused on specific taxa or areas, but our large mammal survey covered the entire protected area and we evaluated the intensity of sampling required to determine population change. Using line transect sampling, we found that the distribution of large mammals was nonrandom and related to habitat‐type. However, confidence intervals of population estimates revealed that much more intensive sampling was required to detect changes in population density at a time scale reasonable for management. For many species, populations would have to decline by 40–60% for this method to detect population change. Post‐stratification decreased confidence intervals of density estimates slightly, increasing our ability to detect change. However, confidence intervals of estimates were still too large to detect a meaningful population change on a time scale that would allow management to take action. Most incidences of illegal activity were about 5 km from the park boundary; however, animal densities were not lower in this area.     

Development of an improved assay for purine nucleoside kinase activity in cell extracts and detection of inosine kinase activity in Brevibacterium acetylicum ATCC 953, related species, and Corynebacterium flaccumfaciens ATCC 6887

An improved assay was developed to detect direct purine nucleoside phosphorylating activity in cell-free extracts. Direct inosine phosphorylating activity was detected in 2 of 70 species tested. Both activities, which depended on magnesium ion and ATP, phosphorylated a hydroxyl group at the 5' position of inosine. The new assay was shown to be useful for screening of direct purine nucleoside phosphorylating activity and have the potential to detect inosine kinase in the presence of a background of nucleoside phosphorylase and purine phosphoribosyltransferase activities. Previously, the latter two activities made it difficult to correctly detect direct phosphorylation of inosine by inosine kinase.     

Detection of Enterobacter sakazakii in dried infant milk formula by cationic-magnetic-bead capture

Enterobacter sakazakii has been associated with life-threatening infections in premature low-birth-weight infants. Contaminated infant milk formula (IMF) has been implicated in cases of E. sakazakii meningitis. Quick and sensitive methods to detect low-level contamination sporadically present in IMF preparations would positively contribute towards risk reduction across the infant formula food chain. Here we report on the development of a simple method, combining charged separation and growth on selective agar, to detect E. sakazakii in IMF. This protocol can reliably detect 1 to 5 CFU of E. sakazakii in 500 g of IMF in less than 24 h.     

Flow cytometric detection of viable bacteria in compost

Abstract Flow cytometry employing several vital stains was used to study the colonisation of sterile compost by Bacillus subtilis 168 (pAB224). The dyes used included rhodamine 123 (Rh123), carboxyfluorescein diacetate (CFDA) and chemchrome B. The results demonstrated the ability of flow cytometry to detect and enumerate viable bacteria in filtered compost extracts. Flow cytometry was also used to detect and study the viability of an indigenous compost community. Although it was possible to detect a viable bacterial population, the numbers of viable bacteria estimated were significantly different to those estimated from cfu.