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.

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.

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

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

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

The compositional and evolutionary logic of metabolism

Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which layers of that system emerged. Metabolism also serves as the foundation in other hierarchies, at least up to cellular integration including bioenergetics and molecular replication, and trophic ecology. The recapitulation of patterns first seen in metabolism, in these higher levels, suggests metabolism as a source of causation or constraint on many forms of organization in the biosphere. We identify as modules widely reused subsets of chemicals, reactions, or functions, each with a conserved internal structure. At the small molecule substrate level, module boundaries are generally associated with the most complex reaction mechanisms and the most conserved enzymes. Cofactors form a structurally and functionally distinctive control layer over the small-molecule substrate. Complex cofactors are often used at module boundaries of the substrate level, while simpler ones participate in widely used reactions. Cofactor functions thus act as "keys" that incorporate classes of organic reactions within biochemistry. The same modules that organize the compositional diversity of metabolism are argued to have governed long-term evolution. Early evolution of core metabolism, especially carbon-fixation, appears to have required few innovations among a small number of conserved modules, to produce adaptations to simple biogeochemical changes of environment. We demonstrate these features of metabolism at several levels of hierarchy, beginning with the small-molecule substrate and network architecture, continuing with cofactors and key conserved reactions, and culminating in the aggregation of multiple diverse physical and biochemical processes in cells.Comment: 56 pages, 28 figure

Experimental M1 Transition Rates of Coronal Lines from Ar X, Ar XIV, and Ar XV

Transition probabilities of three magnetic dipole (M1) transitions in multiply charged ions of Ar have been measured using the Livermore electron-beam ion trap. Two of the transitions are in the ground configurations of Ar XIV (B-like) and Ar IX (F-like), and are associated with the coronal lines at 4412.4 and 5533.4 ÅŽ , respectively. The third is in the excited 2s2p configuration of Be-like Ar XV and produces the coronal line at 5943.73 Å. Our results for the three atomic level lifetimes are 9.32^0.12 ms for the Ar X 2s22p5 2P1/2 level, 9.70^0.15 ms for the Ar XIV 2s22p level, and 15.0^0.8 ms for the Ar XVo 2P3/2o 2s2p level. These results diff†er significantly from earlier measurements and are the most accurate ones to date

Dynamics of tongue microbial communities with single-nucleotide resolution using oligotyping

.© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 5 (2014): 568, doi:10.3389/fmicb.2014.00568.The human mouth is an excellent system to study the dynamics of microbial communities and their interactions with their host. We employed oligotyping to analyze, with single-nucleotide resolution, oral microbial 16S ribosomal RNA (rRNA) gene sequence data from a time course sampled from the tongue of two individuals, and we interpret our results in the context of oligotypes that we previously identified in the oral data from the Human Microbiome Project. Our previous work established that many of these oligotypes had dramatically different distributions between individuals and across oral habitats, suggesting that they represented functionally different organisms. Here we demonstrate the presence of a consistent tongue microbiome but with rapidly fluctuating proportions of the characteristic taxa. In some cases closely related oligotypes representing strains or variants within a single species displayed fluctuating relative abundances over time, while in other cases an initially dominant oligotype was replaced by another oligotype of the same species. We use this high temporal and taxonomic level of resolution to detect correlated changes in oligotype abundance that could indicate which taxa likely interact synergistically or occupy similar habitats, and which likely interact antagonistically or prefer distinct habitats. For example, we found a strong correlation in abundance over time between two oligotypes from different families of Gamma Proteobacteria, suggesting a close functional or ecological relationship between them. In summary, the tongue is colonized by a microbial community of moderate complexity whose proportional abundance fluctuates widely on time scales of days. The drivers and functional consequences of these community dynamics are not known, but we expect they will prove tractable to future, targeted studies employing taxonomically resolved analysis of high-throughput sequencing data sampled at appropriate temporal intervals and spatial scales.Supported by National Institutes of Health (NIH) National Institute of Dental and Craniofacial Research Grant DE022586 (to Gary G. Borisy). Daniel R. Utter was supported by the Woods Hole Partnership Education Program; A. Murat Eren was supported by a G. Unger Vetlesen Foundation grant to the Marine Biological Laboratory; David B. Mark Welch was supported by NSF DBI-126259

QED self-energy contribution to highly-excited atomic states

We present numerical values for the self-energy shifts predicted by QED (Quantum Electrodynamics) for hydrogenlike ions (nuclear charge $60 \le Z \le 110$) with an electron in an $n=3$, 4 or 5 level with high angular momentum ($5/2\le j \le 9/2$). Applications include predictions of precision transition energies and studies of the outer-shell structure of atoms and ions.Comment: 20 pages, 5 figure