FISH Finder: a high-throughput tool for analyzing FISH images

MOTIVATION: Fluorescence in situ hybridization (FISH) is used to study the organization and the positioning of specific DNA sequences within the cell nucleus. Analyzing the data from FISH images is a tedious process that invokes an element of subjectivity. Automated FISH image analysis offers savings in time as well as gaining the benefit of objective data analysis. While several FISH image analysis software tools have been developed, they often use a threshold-based segmentation algorithm for nucleus segmentation. As fluorescence signal intensities can vary significantly from experiment to experiment, from cell to cell, and within a cell, threshold-based segmentation is inflexible and often insufficient for automatic image analysis, leading to additional manual segmentation and potential subjective bias. To overcome these problems, we developed a graphical software tool called FISH Finder to automatically analyze FISH images that vary significantly. By posing the nucleus segmentation as a classification problem, compound Bayesian classifier is employed so that contextual information is utilized, resulting in reliable classification and boundary extraction. This makes it possible to analyze FISH images efficiently and objectively without adjustment of input parameters. Additionally, FISH Finder was designed to analyze the distances between differentially stained FISH probes. AVAILABILITY: FISH Finder is a standalone MATLAB application and platform independent software. The program is freely available from: http://code.google.com/p/fishfinder/downloads/list.     

Pleiotropic effects on mandibular morphology I. Developmental morphological integration and differential dominance

Pleiotropy refers to a single genetic locus that affects more than one phenotypic trait. Pleiotropic effects of genetic loci are thought to play an important role in evolution, reflecting functional and developmental relationships among phenotypes. In a previous study, we examined pleiotropic effects displayed by quantitative trait loci (QTLs) on murine mandibular morphology in relation to mandibular structure and function. In replicating most of our previous QTLs and increasing our sample size, this study strengthens and extends our earlier results. As in our previous study, we find that QTL effects tend to be restricted to developmentally or functionally related traits. In addition, we examine patterns of differential dominance for pleiotropic QTL effects. Differential dominance occurs when dominance patterns for a single locus vary among traits. We find that multivariate overdominance is a common and substantial phenomenon, and may potentially provide an explanation for the persistence of heterozygosity in natural populations.     

Process control and drug analysis with an on-line capillary electrophoresis system

Inorganic and organic ions in pulp and paper process waters and drug mixtures were studied. Real-time measurements and on-line simulated analyses were made. A novel on-line capillary electrophoresis instrument equipped with a fixed wavelength UV detector having a 254-nm filter was used for the analyses. Three dynamic sample and electrolyte micromodules provided on-line sampling, sample introduction and solution feedings. The system was used to monitor process samples containing thiosulphate, chloride, sulphate, oxalate, acetate and carbonate. It approved good performance in separation of ethacrynic acid, furosemide, probenecid, bumetanide and hydrochlorothiazide as well as that of normethanephrine, methanephrine and dopamine standard mixtures. The LOD and LOQ values of the ions and drugs ranged from 0.1 to 1 mg/l for LOD and from 1 to 10 mg/l for LOQ. Sensitivity of the drugs was higher due to the single wavelength available in the system. It required that the drugs were to be identified by indirect UV detection. Repeatability of the analyses was good (RSD% below 5).     

Binary toxins from Bacillus thuringiensis active against the western corn rootworm, Diabrotica virgifera virgifera LeConte

The western corn rootworm, Diabrotica virgifera virgifera LeConte, is a significant pest of corn in the United States. The development of transgenic corn hybrids resistant to rootworm feeding damage depends on the identification of genes encoding insecticidal proteins toxic to rootworm larvae. In this study, a bioassay screen was used to identify several isolates of the bacterium Bacillus thuringiensis active against rootworm. These bacterial isolates each produce distinct crystal proteins with approximate molecular masses of 13 to 15 kDa and 44 kDa. Insect bioassays demonstrated that both protein classes are required for insecticidal activity against this rootworm species. The genes encoding these proteins are organized in apparent operons and are associated with other genes encoding crystal proteins of unknown function. The antirootworm proteins produced by B. thuringiensis strains EG5899 and EG9444 closely resemble previously described crystal proteins of the Cry34A and Cry35A classes. The antirootworm proteins produced by strain EG4851, designated Cry34Ba1 and Cry35Ba1, represent a new binary toxin. Genes encoding these proteins could become an important component of a sustainable resistance management strategy against this insect pest.     

Quantitative trait loci for maternal performance for offspring survival in mice

Maternal performance refers to the effect that the environment provided by mothers has on their offspring's phenotypes, such as offspring survival and growth. Variations in maternal behavior and physiology are responsible for variations in maternal performance, which in turn affects offspring survival. In our study we found females that failed to nurture their offspring and showed abnormal maternal behaviors. The genetic architecture of maternal performance for offspring survival was investigated in 241 females of an F(2) intercross of the SM/J and LG/J inbred mouse strains. Using interval-mapping methods we found two quantitative trait loci (QTL) affecting maternal performance at D2Mit17 + 6 cM and D7Mit21 + 2 cM on chromosomes 2 and 7, respectively. In a two-way genome-wide epistasis scan we found 15 epistatic interactions involving 23 QTL distributed across all chromosomes except 12, 16, and 17. These loci form several small sets of interacting QTL, suggesting a complex set of mechanisms operating to determine maternal performance for offspring survival. Taken all together and correcting for the large number of significant factors, QTL and their interactions explain almost 35% of the phenotypic variation for maternal performance for offspring survival in this cross. This study allowed the identification of many possible candidate genes, as well as the relative size of gene effects and patterns of gene action affecting maternal performance in mice. Detailed behavior observation of mothers from later generations suggests that offspring survival in the first week is related to maternal success in building nests, grooming their pups, providing milk, and/or manifesting aggressive behavior against intruders.     

EPISTASIS AND THE EVOLUTION OF ADDITIVE GENETIC VARIANCE IN POPULATIONS THAT PASS THROUGH A BOTTLENECK

Traditional models of genetic drift predict a linear decrease in additive genetic variance for populations passing through a bottleneck. This perceived lack of heritable variance limits the scope of founder-effect models of speciation. We produced 55 replicate bottleneck populations maintained at two male-female pairs through four generations of inbreeding (average F = 0.39). These populations were formed from an F₂ intercross of the LG/J and SM/J inbred mouse strains. Two contemporaneous control strains maintained with more than 60 mating pairs per generation were formed from this same source population. The average level of within-strain additive genetic variance for adult body weight was compared between the control and experimental lines. Additive genetic variance for adult body weight within experimental bottleneck strains was significantly higher than expected under an additive genetic model This enhancement of additive genetic variance under inbreeding is likely to be due to epistasis, which retards or reverses the loss of additive genetic variance under inbreeding for adult body weight in this population. Therefore, founder-effect speciation processes may not be constrained by a loss of heritable variance due to population bottlenecks.     

Animal board invited review: Animal source foods in healthy,sustainable, and ethical diets – An argument against drastic limitation of livestock in the food system

Animal source foods are evolutionarily appropriate foods for humans. It is therefore remarkable that they are now presented by some as unhealthy, unsustainable, and unethical, particularly in the urban West. The benefits of consuming them are nonetheless substantial, as they offer a wide spectrum of nutrients that are needed for cell and tissue development, function, and survival. They play a role in proper physical and cognitive development of infants, children, and adolescents, and help promote maintenance of physical function with ageing. While high-red meat consumption in the West is associated with several forms of chronic disease, these associations remain uncertain in other cultural contexts or when consumption is part of wholesome diets. Besides health concerns, there is also widespread anxiety about the environmental impacts of animal source foods. Although several production methods are detrimental (intensive cropping for feed, overgrazing, deforestation, water pollution, etc.) and require substantial mitigation, damaging impacts are not intrinsic to animal husbandry. When well-managed, livestock farming contributes to ecosystem management and soil health, while delivering high-quality foodstuffs through the upcycling of resources that are otherwise non-suitable for food production, making use of marginal land and inedible materials (forage, by-products, etc.), integrating livestock and crop farming where possible has the potential to benefit plant food production through enhanced nutrient recycling, while minimising external input needs such as fertilisers and pesticides. Moreover, the impacts on land use, water wastage, and greenhouse gas emissions are highly contextual, and their estimation is often erroneous due to a reductionist use of metrics. Similarly, whether animal husbandry is ethical or not depends on practical specificities, not on the fact that animals are involved. Such discussions also need to factor in that animal husbandry plays an important role in culture, societal well-being, food security, and the provision of livelihoods. We seize this opportunity to argue for less preconceived assumptions about alleged effects of animal source foods on the health of the planet and the humans and animals involved, for less top-down planning based on isolated metrics or (Western) technocratic perspectives, and for more holistic and circumstantial approaches to the food system.     

Acute effect of whole-body vibration on electromechanical delay and vertical jump performance

Objectives:To determine if a change in vertical jump performance from acute whole-body vibration can be explained by indirectly assessing spindle sensitivity from electromechanical delay.Methods:Using a counter-balanced design, twenty college-aged participants performed whole-body vibration (WBV) and control treatments. WBV included 10 intervals (26 Hz, 3.6 mm) of 60 s in a half-squat followed by 60 s of rest. After 5 intervals, participants rested for 6-minutes before commencing the final 5 intervals. For the control, the exact same protocol of whole-body vibration was performed but without vibration. Electromechanical delay and vertical jump were assessed at baseline, during the 6-minute rest period and immediately after whole-body vibration and control.Results:There were no differences between treatments, for both electromechanical delay (F(2, 38)=1.385, p=0.263) and vertical jump (F(2, 38)=0.040, p<0.96). Whole-body vibration had no effect on vertical jump performance.Conclusion:The current whole-body vibration protocol is not effective for acute vertical jump or electromechanical delay enhancement. Also, since there was no effect on electromechanical delay, this suggests that whole-body vibration did not enhance muscle spindle sensitivity for the parameters examined.