Comparison of microfluidic digital PCR and conventional quantitative PCR for measuring copy number variation

One of the benefits of Digital PCR (dPCR) is the potential for unparalleled precision enabling smaller fold change measurements. An example of an assessment that could benefit from such improved precision is the measurement of tumour-associated copy number variation (CNV) in the cell free DNA (cfDNA) fraction of patient blood plasma. To investigate the potential precision of dPCR and compare it with the established technique of quantitative PCR (qPCR), we used breast cancer cell lines to investigate HER2 gene amplification and modelled a range of different CNVs. We showed that, with equal experimental replication, dPCR could measure a smaller CNV than qPCR. As dPCR precision is directly dependent upon both the number of replicate measurements and the template concentration, we also developed a method to assist the design of dPCR experiments for measuring CNV. Using an existing model (based on Poisson and binomial distributions) to derive an expression for the variance inherent in dPCR, we produced a power calculation to define the experimental size required to reliably detect a given fold change at a given template concentration. This work will facilitate any future translation of dPCR to key diagnostic applications, such as cancer diagnostics and analysis of cfDNA.     

Sea-Age Variation in Maiden Atlantic Salmon Spawners: Phenotypic Plasticity or Genetic Polymorphism?

Atlantic salmon exhibit a partially heritable polymorphism in which the morphs are distinguished by the duration and location of the sea-phase of their life-cycle. These morphs co-occur, albeit in characteristically different proportions, in most Scottish rivers and in both the spring and autumn spawner runs; early running fish being generally associated with upland spawning locations while late running fish are associated with lowland spawning. Thus, differences in riverine and marine environment appear to be linked to differences in the relative abundance of the morphs, rather than to the specific morph which is optimally adapted. In this paper, we report a model-based synthetic study aimed at understanding the key dynamic elements which determine the long-term stability of this polymorphism, and thus determine the relative abundance of the various sea-age morphs. Given the recent accumulation of evidence for a genetic basis for the polymorphism, we argue that the key dynamic mechanism which equalises the realized fitness of the sea-age morphs must be one or more morph-specific density dependencies in the riverine phase of the life-history. We explore a number of specific mechanisms, firmly based in known salmon biology, by which such morph-specific density dependence could occur and investigate the robustness of the co-existence which they imply. We conclude that the co-occurrence of multiple sea-age morphs of Atlantic salmon in Scottish rivers is a stable genetic polymorphism, maintained by some combination of physical separation and asymmetric competition between spawners of different morphs or the riverine stages of their offspring or both.     

Stress distribution and consolidation in cartilage constituents is influenced by cyclic loading and osteoarthritic degeneration

The understanding of load support mechanisms in cartilage has evolved with computational models that better mimic the tissue ultrastructure. Fibril-reinforced poroelastic models can reproduce cartilage behaviour in a variety of test conditions and can be used to model tissue anisotropy as well as assess stress and pressure partitioning to the tissue constituents. The goal of this study was to examine the stress distribution in the fibrillar and non-fibrillar solid phase and pressure in the fluid phase of cartilage in axisymmetric models of a healthy and osteoarthritic hip joint. Material properties, based on values from the literature, were assigned to the fibrillar and poroelastic components of cartilage and cancellous and subchondral compact bone regions. A cyclic load representing walking was applied for 25 cycles. Contact stresses in the fibrillar and non-fibrillar solid phase supported less than 1% of the contact force and increased only minimally with load cycles. Simulated proteoglycan depletion increased stresses in the radial and tangential collagen fibrils, whereas fibrillation of the tangential fibrils resulted in increased compressive stress in the non-fibrillar component and tensile stress in the radial fibrils. However neither had an effect on fluid pressure. Subchondral sclerosis was found to have the largest effect, resulting in increased fluid pressure, non-fibrillar compressive stress, tangential fibril stress and greater cartilage consolidation. Subchondral bone stiffening may play an important role in the degenerative cascade and may adversely affect tissue repair and regeneration treatments.     

Reliability of knee joint muscle activity during weight bearing force control

We developed a novel approach that requires subjects to produce and finely tune ground reaction forces (GRFs) while standing. The aim of this study was to examine the reliability of electromyographic data recorded during these tasks. Healthy young adults stood with their dominant leg in a boot fixed to a force platform. A target matching protocol required subjects to control both the direction and magnitude of GRF along the horizontal plane while maintaining constant inferior–superior loads of 50% body-weight (BW). Each target matching task was repeated three times in a random order. Subjects were retested with the same protocol 2–3 days later. Normalised electromyography data of eight muscles crossing the knee joint was collected for each successful target match. A random model, single measures intra-class correlation analysed the reliability for both test–retest and intra-day results, in addition to inter-subject reliability. The GRFs required to meet the targets were comparable to a range of activities of daily living, ranging from 0.48 to 0.58 N/kg of BW in the horizontal plane while maintaining 50% BW in the vertical plane. We observed moderate to high ICC values (0.60–0.993) for most muscles in most directions, indicating low within-subject variance. In addition, moderate to high between-subject reliability was observed in all eight muscle activation profiles, indicating subjects used similar neuromuscular control strategies to achieve the desired GRFs. In conclusion, our protocol identifies non-random weight-bearing motor control strategies while generating direction dependent GRFs. These results provide reliable insight into knee joint stabilisation strategies during weight bearing.     

The reaction between some dyes and synthetic hydroxyapatite I. The uptake of dyes in relation to their structures

Synopsis The uptake of dyes from dilute solutions by synthetic hydroxyapatite and other sparingly soluble calcium compounds has been determined. About 30 dyes, mostly azo-, dis-azo and anthraquinonoid types were used in 95% ethanol or 0.1 M tris buffer. Many had closely related configurations. Chemical groupings possibly responsible for the adsorption of particular dyes by hydroxyapatite have been deduced from an analysis of the results. The uptake of most dyes from alcoholic solutions was, linearly related to the surface area of hydroxyapatite. Calcium carbonate and secondary calcium phosphate took up less stain than hydroxyapatite of similar surface area. With the simpler anthraquinonoid dyes, the uptake was higher from aqueous than alcoholic solutions, but specificity for hydroxyapatite was much less. The increased uptake of dye by powdered bone or dentine when rendered anorganic was proportional to the increased surface area. It was found that several dyes in common use as stains for bone and calcified tissue were only poorly adsorbed by synthetic hydroxyapatite under the particular conditions of these experiments.The experimental data presented could be used as a basis for the development of histochemical reactions for calcified tissue or inclusions. By suitable choice of dyes, solvent and rinsing solution it ought to be possible to differentiate various forms of calcified material.