Manual for starch gel electrophoresis: A method for the detection of genetic variation

The procedure to conduct horizontal starch gel electrophoresis on enzymes is described in detail. Areas covered are (I) collection and storage of specimens, (2) preparation of tissues, (3) preparation of a starch gel, (4) application of enzyme extracts to a gel, (5) setting up a gel for electrophoresis, (6) slicing a gel, and (7) staining a gel. Recipes are also included for 47 enzyme stains and 3 selected gel buffers. (PDF file contains 26 pages.

Photoelastic force measurements in granular materials

Photoelastic techniques are used to make both qualitative and quantitative measurements of the forces within idealized granular materials. The method is based on placing a birefringent granular material between a pair of polarizing filters, so that each region of the material rotates the polarization of light according to the amount of local of stress. In this review paper, we summarize past work using the technique, describe the optics underlying the technique, and illustrate how it can be used to quantitatively determine the vector contact forces between particles in a 2D granular system. We provide a description of software resources available to perform this task, as well as key techniques and resources for building an experimental apparatus

Signatures of natural selection among lineages and habitats in Oncorhynchus mykiss

Recent advances in molecular interrogation techniques now allow unprecedented genomic inference about the role of adaptive genetic divergence in wild populations. We used high-throughput genotyping to screen a genome-wide panel of 276 single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonid Oncorhynchus mykiss. Samples included 805 individuals from 11 anadromous and resident populations from the northwestern United States and British Columbia, and represented two major lineages including paired populations of each life history within single drainages of each lineage. Overall patterns of variation affirmed clear distinctions between lineages and in most instances, isolation by distance within them. Evidence for divergent selection at eight candidate loci included significant landscape correlations, particularly with temperature. High diversity of two nonsynonymous mutations within the peptide-binding region of the major histocompatibility complex (MHC) class II (DAB) gene provided signatures of balancing selection. Weak signals for potential selection between sympatric resident and anadromous populations were revealed from genome scans and allele frequency comparisons. Our results suggest an important adaptive role for immune-related functions and present a large genomic resource for future studie

The Behavior of Granular Materials under Cyclic Shear

The design and development of a parallel plate shear cell for the study of large scale shear flows in granular materials is presented. The parallel plate geometry allows for shear studies without the effects of curvature found in the more common Couette experiments. A system of independently movable slats creates a well with side walls that deform in response to the motions of grains within the pack. This allows for true parallel plate shear with minimal interference from the containing geometry. The motions of the side walls also allow for a direct measurement of the velocity profile across the granular pack. Results are presented for applying this system to the study of transients in granular shear and for shear-induced crystallization. Initial shear profiles are found to vary from packing to packing, ranging from a linear profile across the entire system to an exponential decay with a width of approximately 6 bead diameters. As the system is sheared, the velocity profile becomes much sharper, resembling an exponential decay with a width of roughly 3 bead diameters. Further shearing produces velocity profiles which can no longer be fit to an exponential decay, but are better represented as a Gaussian decay or error function profile. Cyclic shear is found to produce large scale ordering of the granular pack, which has a profound impact on the shear profile. There exist periods of time in which there is slipping between layers as well as periods of time in which the layered particles lock together resulting in very little relative motion.Comment: 10 pages including 12 figure

Memory of the Unjamming Transition during Cyclic Tiltings of a Granular Pile

Discrete numerical simulations are performed to study the evolution of the micro-structure and the response of a granular packing during successive loading-unloading cycles, consisting of quasi-static rotations in the gravity field between opposite inclination angles. We show that internal variables, e.g., stress and fabric of the pile, exhibit hysteresis during these cycles due to the exploration of different metastable configurations. Interestingly, the hysteretic behaviour of the pile strongly depends on the maximal inclination of the cycles, giving evidence of the irreversible modifications of the pile state occurring close to the unjamming transition. More specifically, we show that for cycles with maximal inclination larger than the repose angle, the weak contact network carries the memory of the unjamming transition. These results demonstrate the relevance of a two-phases description -strong and weak contact networks- for a granular system, as soon as it has approached the unjamming transition.Comment: 13 pages, 15 figures, soumis \`{a} Phys. Rev.

Quasiperiodic Tip Splitting in Directional Solidification

We report experimental results on the tip splitting dynamics of seaweed growth in directional solidification of succinonitrile alloys with poly(ethylene oxide) or acetone as solutes. The seaweed or dense branching morphology was selected by solidifying grains which are oriented close to the {111} plane. Despite the random appearance of the growth, a quasiperiodic tip splitting morphology was observed in which the tip alternately splits to the left and to the right. The tip splitting frequency f was found to be related to the growth velocity V as a power law f V^{1.5}. This finding is consistent with the predictions of a tip splitting model that is also presented. Small anisotropies are shown to lead to different kinds of seaweed morphologies.Comment: 4 pages, 7 figures, submitted to Physical Review Letter

On the Application of a Monolithic Array for Detecting Intensity-Correlated Photons Emitted by Different Source Types

It is not widely appreciated that many subtleties are involved in the accurate measurement of intensity-correlated photons; even for the original experiments of Hanbury Brown and Twiss (HBT). Using a monolithic 4x4 array of single-photon avalanche diodes (SPADs), together with an off-chip algorithm for processing streaming data, we investigate the difficulties of measuring second-order photon correlations g2 in a wide variety of light fields that exhibit dramatically different correlation statistics: a multimode He-Ne laser, an incoherent intensity-modulated lamp-light source and a thermal light source. Our off-chip algorithm treats multiple photon-arrivals at pixel-array pairs, in any observation interval, with photon fluxes limited by detector saturation, in such a way that a correctly normalized g2 function is guaranteed. The impact of detector background correlations between SPAD pixels and afterpulsing effects on second-order coherence measurements is discussed. These results demonstrate that our monolithic SPAD array enables access to effects that are otherwise impossible to measure with stand-alone detectors.Comment: 17 pages, 6 figure

Force distributions in a triangular lattice of rigid bars

We study the uniformly weighted ensemble of force balanced configurations on a triangular network of nontensile contact forces. For periodic boundary conditions corresponding to isotropic compressive stress, we find that the probability distribution for single-contact forces decays faster than exponentially. This super-exponential decay persists in lattices diluted to the rigidity percolation threshold. On the other hand, for anisotropic imposed stresses, a broader tail emerges in the force distribution, becoming a pure exponential in the limit of infinite lattice size and infinitely strong anisotropy.Comment: 11 pages, 17 figures Minor text revisions; added references and acknowledgmen

Self-diffusion in dense granular shear flows

Diffusivity is a key quantity in describing velocity fluctuations in granular materials. These fluctuations are the basis of many thermodynamic and hydrodynamic models which aim to provide a statistical description of granular systems. We present experimental results on diffusivity in dense, granular shear in a 2D Couette geometry. We find that self-diffusivities are proportional to the local shear rate with diffusivities along the mean flow approximately twice as large as those in the perpendicular direction. The magnitude of the diffusivity is D \approx \dot\gamma a^2 where a is the particle radius. However, the gradient in shear rate, coupling to the mean flow, and drag at the moving boundary lead to particle displacements that can appear sub- or super-diffusive. In particular, diffusion appears superdiffusive along the mean flow direction due to Taylor dispersion effects and subdiffusive along the perpendicular direction due to the gradient in shear rate. The anisotropic force network leads to an additional anisotropy in the diffusivity that is a property of dense systems with no obvious analog in rapid flows. Specifically, the diffusivity is supressed along the direction of the strong force network. A simple random walk simulation reproduces the key features of the data, such as the apparent superdiffusive and subdiffusive behavior arising from the mean flow, confirming the underlying diffusive motion. The additional anisotropy is not observed in the simulation since the strong force network is not included. Examples of correlated motion, such as transient vortices, and Levy flights are also observed. Although correlated motion creates velocity fields qualitatively different from Brownian motion and can introduce non-diffusive effects, on average the system appears simply diffusive.Comment: 13 pages, 20 figures (accepted to Phys. Rev. E

National Athletic Trainers\u27 Association Position Statement: Safe Weight Loss and Maintenance Practices in Sport and Exercise

Objective: To present athletic trainers with recommendations for safe weight loss and weight maintenance practices for athletes and active clients and to provide athletes, clients, coaches, and parents with safe guidelines that will allow athletes and clients to achieve and maintain weight and body composition goals. Background: Unsafe weight management practices can compromise athletic performance and negatively affect health. Athletes and clients often attempt to lose weight by not eating, limiting caloric or specific nutrients from the diet, engaging in pathogenic weight control behaviors, and restricting fluids. These people often respond to pressures of the sport or activity, coaches, peers, or parents by adopting negative body images and unsafe practices to maintain an ideal body composition for the activity. We provide athletic trainers with recommendations for safe weight loss and weight maintenance in sport and exercise. Although safe weight gain is also a concern for athletic trainers and their athletes and clients, that topic is outside the scope of this position statement. Recommendations: Athletic trainers are often the source of nutrition information for athletes and clients; therefore, they practices, and methods to change body composition. Body composition assessments should be done in the most scientifically appropriate manner possible. Reasonable and individualized weight and body composition goals should be identified by appropriately trained health care personnel (eg, athletic trainers, registered dietitians, physicians). In keeping with the American Dietetics Association (ADA) preferred nomenclature, this document uses the terms registered dietitian or dietician when referring to a food and nutrition expert who has met the academic and professional requirements specified by the ADA\u27s Commission on Accreditation for Dietetics Education. In some cases, a registered nutritionist may have equivalent credentials and be the commonly used term. All weight management and exercise protocols used to achieve these goals should be safe and based on the most current evidence. Athletes, clients, parents, and coaches should be educated on how to determine safe weight and body composition so that athletes and clients more safely achieve competitive weights that will meet sport and activity requirements while also allowing them to meet their energy and nutritional needs for optimal health and performance