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.

Gene duplication in the family Salmonidae 111. Linkage between two duplicated loci coding for aspartate aminotransferase in the cutthroat trout (\u3ci\u3eSalmo clarki\u3c/i\u3e)

The genetic control of the supernatant form of aspartate aminotransferase (AAT) was studied in the cutthroat trout (Salmo clarki) through a series of experimental matings. 509 individuals of eight families were examined to determine (1) the number of loci, (2) the mode of inheritance (i.e. disomic or tetrasomic), and (3) the linkage relationship of the loci involved. The variation observed is controlled by a duplicated locus resulting from a presumed tetraploid event of an ancestral salmonid. The inheritance experiments revealed .the presence of two disomic loci rather than a single tetrasomic locus. indicating that disomy has been reestablished for the chromosomes carrying the AAT loci. The two families in which linkage between these loci could be tested displayed significant nonrandom segregation between these loci with an estimated frequency of recombination of 30.6x,. These results are discussed in regard to the proposed evolution of tetraploidy in the family Salmonidae

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

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

Exploring the protist microbiome: the diversity of bacterial communities associated with Arcella spp. (Tubulina: Amoebozoa)

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gomaa, F., Utter, D. R., Loo, W., Lahr, D. J. G., & Cavanaugh, C. M. Exploring the protist microbiome: the diversity of bacterial communities associated with Arcella spp. (Tubulina: Amoebozoa). European Journal of Protistology, 82, (2022): 125861, https://doi.org/10.1016/j.ejop.2021.125861.Research on protist-bacteria interactions is increasingly relevant as these associations are now known to play important roles in ecosystem and human health. Free-living amoebae are abundant in all environments and are frequent hosts for bacterial endosymbionts including pathogenic bacteria. However, to date, only a small fraction of these symbionts have been identified, while the structure and composition of the total symbiotic bacterial communities still remains largely unknown. Here, we use the testate amoeba Arcella spp. as model organisms to investigate the specificity and diversity of Arcella-associated microbial communities. High-throughput amplicon sequencing from the V4 region of the 16S rRNA gene revealed high diversity in the bacterial communities associated with the wild Arcella spp. To investigate the specificity of the associated bacterial community with greater precision, we investigated the bacterial communities of two lab-cultured Arcella species, A. hemispherica and A. intermedia, grown in two different media types. Our results suggest that Arcella-bacteria associations are species-specific, and that the associated bacterial community of lab-cultured Arcella spp. remains distinct from that of the surrounding media. Further, each host Arcella species could be distinguished based on its bacterial composition. Our findings provide insight into the understanding of eukaryotic-bacterial symbiosis.This project was funded by National Science Foundation Postdoctoral Research Fellowship in Biology to F. Gomaa, Grant Number: PRFB1611514. Support was provided to D.R.U. from the National Science Foundation Graduate Research Fellowship Program under Grant No. DGE1745303 to D.R.U and by Harvard University’s Department of Organismic and Evolutionary Biology program

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

Role of a cdk5-associated protein, p35, in herpes simplex virus type 1 replication in vivo

Previous studies have shown that herpes simplex virus type 1 (HSV-1) replication is inhibited by the cyclin-dependent kinase (cdk) inhibitor roscovitine. One roscovitine-sensitive cdk that functions in neurons is cdk5, which is activated in part by its binding partner, p35. Because HSV establishes latent infections in sensory neurons, we sought to determine the role p35 plays in HSV-1 replication in vivo. For these studies, wild-type (wt) and p35-/- mice were infected with HSV-1 using the mouse ocular model of HSV latency and reactivation. The current results indicate that p35 is an important determinant of viral replication in vivo

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.

Improved electron-beam ion-trap lifetime measurement of the Ne8+ 1s2s3S1 level

An earlier electron-beam ion-trap (EBIT) lifetime measurement of the Ne8+ 1s2s3S1 level has been improved upon, reducing the uncertainties to less than the scatter in the existing theoretical calculations. The new result, 91.7±0.4 μs, agrees with the previous value, but is more precise by a factor of 4. The new value distinguishes among theoretical values, as agreement is obtained only with those calculations that employ "exact" nonrelativistic or relativistic wave functions. Routes to measurements with even higher accuracy are discussed