Obtaining Xenopus laevis Embryos.

The embryos of the African clawed frog, Xenopus laevis, are a powerful substrate for the study of complex fundamental biological and disease mechanisms in neurobiology, physiology, molecular biology, cell biology, and developmental biology. A simple and straightforward technique for generating a large number of developmentally synchronized embryos is in vitro fertilization (IVF). IVF permits simultaneous fertilization of thousands of eggs but requires the death of the parental male, which may not be feasible if the male comes from a stock of precious animals. An alternative to euthanizing a precious male is to use a natural mating, which allows for the collection of many embryos with minimal preparation but with the potential loss of the experimental advantage of developmental synchronization. Here we present both strategies for obtaining X. laevis embryos.

Obtaining Xenopus laevis Eggs.

Nearly a century ago, studies by Lancelot Hogben and others demonstrated that ovulation in female Xenopus laevis can be induced via injection of mammalian gonadotropins into the dorsal lymph sac, allowing for egg production throughout the year independent of the normal reproductive cycles. Hormonally induced females are capable of producing thousands of eggs in a single spawning, which can then be fertilized to generate embryos or used as a substrate for generation of egg extracts. The protocol for induction of ovulation and subsequent egg collection is straightforward and robust, yet some of its details may vary among laboratories based on prior training, availability of necessary reagents, or the experimental objectives. As the goal of this protocol is not to describe every single variation possible for acquiring eggs but to provide a simple and clear description that can be easily applied by researchers with no prior working experience with X. laevis, we focus on describing the method we use at the National Xenopus Resource-that is, inducing ovulation in X. laevis via dorsal lymph sac injection of gonadotropic hormones and the stimulation of egg laying through application of gentle pressure to the females.

Animal Maintenance Systems: Xenopus laevis.

Modular recirculating animal aquaculture systems incorporate UV sterilization and biological, mechanical, and activated carbon filtration, creating a nearly self-contained stable housing environment for Xenopus laevis Nonetheless, minimal water exchange is necessary to mitigate accumulation of metabolic waste, and regular weekly, monthly, and yearly maintenance is needed to ensure accurate and efficient operation. This protocol describes the methods for establishing a new recirculating system and the necessary maintenance, as well as water quality parameters, required for keeping Xenopus laevis.

Animal Maintenance Systems: Xenopus tropicalis.

Modular recirculating animal aquaculture systems incorporate UV sterilization and biological, mechanical, and activated carbon filtration, creating a nearly self-contained stable housing environment for Xenopus tropicalis Nonetheless, minimal water exchange is necessary to mitigate accumulation of metabolic waste, and regular weekly, monthly, and yearly maintenance is needed to ensure accurate and efficient operation. This protocol describes the methods for establishing a new recirculating system and the necessary maintenance, as well as water quality parameters, required for keeping Xenopus tropicalis.

Supporting the health library and information workforce.

As a prelude to his keynote speech at the forthcoming Health Libraries Group conference, Sean McNamara, Head of CILIP Scotland, provides an insight into the work being undertaken with health librarians in Scotland and considers how CILIP Scotland might support the health information sector in the coming years.

Xenopus Resources: Transgenic, Inbred and Mutant Animals, Training Opportunities, and Web-Based Support.

Two species of the clawed frog family, Xenopus laevis and X. tropicalis, are widely used as tools to investigate both normal and disease-state biochemistry, genetics, cell biology, and developmental biology. To support both frog specialist and non-specialist scientists needing access to these models for their research, a number of centralized resources exist around the world. These include centers that hold live and frozen stocks of transgenic, inbred and mutant animals and centers that hold molecular resources. This infrastructure is supported by a model organism database. Here, we describe much of this infrastructure and encourage the community to make the best use of it and to guide the resource centers in developing new lines and libraries.

Use of a Hepatitis C Screening Order Set to Improve Screening Rates and Measure Intervention Effectiveness.

INTRODUCTION: Hepatitis C virus (HCV) infection leads to significant morbidity and mortality. Rates of HCV infection are greatest in patients born from 1945 to 1965, so the Centers for Disease Control recommends a one-time screening in this cohort. Previous interventions utilizing the electronic medical record (EMR) capabilities at two University of Utah Family Medicine clinics have increased screening rates significantly, but further improvement is possible. METHODS: A family medicine resident-led continuous quality improvement (CQI) team used the Model for Improvement methods popularized by the Institute for Healthcare Improvement to create a team-based intervention with the goal of improving HCV screening in a family medicine faculty and resident clinic. An order set was created and a protocol developed that allowed medical assistants or clinic phlebotomists to order the appropriate HCV screening lab if this had not yet been done by the primary care provider. Data were extracted from the EMR that showed changes in total and monthly screening rates as well as the frequency of order set use. RESULTS: Monthly screening rates at the Madsen Family Medicine Clinic (Salt Lake City, UT) increased from approximately 40% to greater than 50% in the 5-month intervention period. The order set was used 19 times during this period which accounted for 18.8% of new screens. CONCLUSIONS: Creating an order set that allows medical assistants to order the HCV screening lab increased HCV screening rates in our clinic. Because order set utilization data can be extracted from the EMR, this intervention provided a process measure that can differentiate the effect of this intervention from the effects of other interventions previously undertaken in the clinic.

Husbandry, General Care, and Transportation of Xenopus laevis and Xenopus tropicalis.

Maintenance of optimal conditions such as water parameters, diet, and feeding is essential to a healthy Xenopus laevis and Xenopus tropicalis colony and thus to the productivity of the lab. Our prior husbandry experience as well as the rapid growth of the National Xenopus Resource has given us a unique insight into identifying and implementing these optimal parameters into our husbandry operations. Here, we discuss our standard operating procedures that will be of use to both new and established Xenopus facilities.

Generation and Care of Xenopus laevis and Xenopus tropicalis Embryos.

Robust and efficient protocols for fertilization and early embryo care of Xenopus laevis and Xenopus tropicalis are essential for experimental success, as well as maintenance and propagation of precious animal stocks. The rapid growth of the National Xenopus Resource has required effective implementation and optimization of these protocols. Here, we discuss the procedures used at the National Xenopus Resource, which we found helpful for generation and early upkeep of Xenopus embryos and tadpoles.

Eshelby inclusions in granular matter: Theory and simulations.

We present a numerical implementation of an active inclusion in a granular material submitted to a biaxial test. We discuss the dependence of the response to this perturbation on two parameters: the intragranular friction coefficient on one hand, and the degree of the loading on the other hand. We compare the numerical results to theoretical predictions taking into account the change of volume of the inclusion as well as the anisotropy of the elastic matrix.

Emergence of cooperativity in plasticity of soft glassy materials.

The elastic coupling between plastic events is generally invoked to interpret plastic properties and the failure of amorphous soft glassy materials. We report an experiment where the emergence of a self-organized plastic flow is observed well before the failure. For this we impose an homogeneous stress on a granular material, and measure local deformations for very small strain increments using a light scattering setup. We observe a nonhomogeneous strain that appears as transient bands of mesoscopic size and a well-defined orientation, which is different from the angle of the macroscopic frictional shear band that appears at the failure. The presence and the orientation of those microbands may be understood by considering how localized plastic reorganizations redistribute stresses in a surrounding continuous elastic medium. We characterize the length scale and persistence of the structure. The presence of plastic events and the mesostructure of the plastic flow are compared to numerical simulations.

Relevance of numerical simulations to booming sand.

We have performed a simulation study of three-dimensional cohesionless granular flows down an inclined chute. We find that the oscillations observed in [L. E. Silbert, Phys. Rev. Lett. 94, 098002 (2005)] near the angle of repose are harmonic vibrations of the lowest normal mode. Their frequencies depend on the contact stiffness as well as on the depth of the flow. Could these oscillations account for the phenomena of "booming sand"? We estimate an effective contact stiffness from the Hertz law, but this leads to frequencies that are several times higher than observed. However, the Hertz law also predicts interpenetrations of a few nanometers, indicating that the oscillations frequencies are governed by the surface stiffness, which can be much lower than the bulk one. This is in agreement with previous studies ascribing the ability to sing to the presence of a soft coating on the grain surface.

Land-use intensification reduces functional redundancy and response diversity in plant communities.

Ecosystem resilience depends on functional redundancy (the number of species contributing similarly to an ecosystem function) and response diversity (how functionally similar species respond differently to disturbance). Here, we explore how land-use change impacts these attributes in plant communities, using data from 18 land-use intensity gradients that represent five biomes and > 2800 species. We identify functional groups using multivariate analysis of plant traits which influence ecosystem processes. Functional redundancy is calculated as the species richness within each group, and response diversity as the multivariate within-group dispersion in response trait space, using traits that influence responses to disturbances. Meta-analysis across all datasets showed that land-use intensification significantly reduced both functional redundancy and response diversity, although specific relationships varied considerably among the different land-use gradients. These results indicate that intensified management of ecosystems for resource extraction can increase their vulnerability to future disturbances.

Measurement of granular entropy.

Recently, Dean and Lefèvre [Phys. Rev. Lett. 90, 198301 (2003)] developed a method for testing the statistical mechanical theory of granular packings proposed by Edwards and co-workers [Physica A 157, 1080 (1989); Phys. Rev. E 58, 4758 (1998)]. The method relies on the prediction that the ratio of two overlapping volume histograms should be exponential in volume. We extend the method by showing that one can also calculate the entropy of the packing and also that the method can yield false positive results when the histograms are Gaussians with nearly identical variances. We then apply the method to simulations and experiments of granular compaction. The distribution of global volumes (the volume of the entire packing) is nearly Gaussian and it is difficult to conclude if the theory is valid. On the other hand, the distribution of Voronoï volumes clearly obeys the theoretical prediction.

What triggers failure in frictional granular assemblies?

We examine numerically the yielding or failure of small granular packings subjected to an increasing deviatoric stress. As the load increases, the packing softens and the number of sliding contacts rises. When the packing fails, the kinetic energy starts to rise exponentially in time. It is always possible to identify a contact status change that triggers the collapse of the packing. Furthermore, by use of the stiffness matrix, we show that this change often causes a mechanical instability or a motion with neutral stability. In some cases, the status change provokes an oscillation and a second status change following shortly thereafter introduces an instability. Failure can also be considered from the perspective of energy flux: before failure, the energy injected by the load is stored as potential energy in the contacts. When this is no longer possible, failure occurs and the injected energy is converted to kinetic energy. However, the force disequilibrium then soon becomes the dominant energy source.

Quasirigidity: some uniqueness issues.

Quasirigidity means that one builds a theory for assemblies of grains under a slowly changing external load by using the deformation of those grains as a small parameter. Is quasirigidity a complete theory for these granular assemblies? Does it provide unique predictions of the assembly's behavior, or must some other process be invoked to decide between several possibilities? We provide evidence that quasirigidity is a complete theory by showing that two possible sources of indeterminacy do not exist for the case of disk-shaped grains. One possible source of indeterminacy arises from zero-frequency modes present in the packing. This problem can be solved by considering the conditions required to obtain force equilibrium. A second possible source of indeterminacy is the necessity to choose the status (sliding or nonsliding) at each contact. We show that only one choice is permitted, if contacts slide only when required by Coulomb friction.

Indeterminacy and the onset of motion in a simple granular packing.

We examine the relatively simple problem of a disk placed in a symmetric V-shaped channel, and subjected to gravity and a torque. We obtain analytic predictions of the contact forces and disk motion using two different models. In the first model, the disk is assumed to be perfectly rigid, leading to force indeterminacy. In the second model, the disk is assumed to interact with the walls of the channel via linear springs, leading to a unique solution for the contact forces. The results of these two models are compared. It is shown that there are two possible ways motion can occur--through the appearance of a null eigenvector of the stiffness matrix, or through an instability. When motion occurs through an instability, the first model cannot predict when the disk will rotate; it is necessary to know the undetermined forces in order to predict the motion of the disk. It is also shown how indeterminacy in the first model is linked to memory in the second. The analytical results are also compared with numerical simulations using two different methods, each related to one of the models.

Simulations of vibrated granular medium with impact-velocity-dependent restitution coefficient.

We report numerical simulations of strongly vibrated granular materials designed to mimic recent experiments performed in both the presence and the absence of gravity. The coefficient of restitution used here depends on the impact velocity by taking into account both the viscoelastic and plastic deformations of particles, occurring at low and high velocities, respectively. We show that this model with impact-velocity-dependent restitution coefficient reproduces results that agree with experiments. We measure the scaling exponents of the granular temperature, collision frequency, impulse, and pressure with the vibrating piston velocity as the particle number increases. As the system changes from a homogeneous gas state at low density to a clustered state at high density, these exponents are all found to decrease continuously with increasing particle number. All these results differ significantly from classical inelastic hard sphere kinetic theory and previous simulations, both based on a constant restitution coefficient.