Estimating the degree of saturation in mutant screens

Large-scale screens for loss-of-function mutants have played a significant role in recent advances in developmental biology and other fields. In such mutant screens, it is desirable to estimate the degree of saturation of the screen (i.e., what fraction of the possible target genes has been identified). We applied Bayesian and maximum-likelihood methods for estimating the number of loci remaining undetected in large-scale screens and produced credibility intervals to assess the uncertainty of these estimates. Since different loci may mutate to alleles with detectable phenotypes at different rates, we also incorporated variation in the degree of mutability among genes, using either gamma-distributed mutation rates or multiple discrete mutation rate classes. We examined eight published data sets from large-scale mutant screens and found that credibility intervals are much broader than implied by previous assumptions about the degree of saturation of screens. The likelihood methods presented here are a significantly better fit to data from published experiments than estimates based on the Poisson distribution, which implicitly assumes a single mutation rate for all loci. The results are reasonably robust to different models of variation in the mutability of genes. We tested our methods against mutant allele data from a region of the Drosophila melanogaster genome for which there is an independent genomics-based estimate of the number of undetected loci and found that the number of such loci falls within the predicted credibility interval for our models. The methods we have developed may also be useful for estimating the degree of saturation in other types of genetic screens in addition to classical screens for simple loss-of-function mutants, including genetic modifier screens and screens for protein-protein interactions using the yeast two-hybrid method

Application of Dynamic System Identification to Timber Bridges

A method of global nondestructive evaluation for identifying local damage and decay in timber beams was developed in previous analytical studies and verified experimentally using simply supported beams in the laboratory. The method employs experimental modal analysis and an algorithm that monitors changes in modal strain energy between the mode shapes of a damaged structure with respect to the undamaged structure. A simple three-girder bridge was built and tested in a laboratory to investigate the capability and limitations of the method for detecting damage in a multimember timber structure. The laboratory tests showed that the method can correctly detect and locate a simulated pocket of decay inflicted at the end of a girder as well as detect a notch removed from the midspan of a girder. The tests showed that the method can correctly detect damage simultaneously at two locations within the bridge, but also that large magnitudes of damage at one location can mask smaller magnitudes of damage at another location. When a calibrated baseline model is used to represent the undamaged state of the bridge, the results show that the method of nondestructive evaluation is able to detect each case of inflicted damage, but with some increase in localization error

Functionality and the evolution of marginal stability in proteins: Inferences from lattice simulations

It has been known for some time that many proteins are marginally stable. This has inspired several explanations. Having noted that the functionality of many enzymes is correlated with subunit motion, flexibility, or general disorder, some have suggested that marginally stable proteins should have an evolutionary advantage over proteins of differing stability. Others have suggested that stability and functionality are contradictory qualities, and that selection for both criteria results in marginally stable proteins, optimised to satisfy the competing design pressures. While these explanations are plausible, recent research simulating the evolution of model proteins has shown that selection for stability, ignoring any aspects of functionality, can result in marginally stable proteins because of the underlying makeup of protein sequence-space. We extend this research by simulating the evolution of proteins, using a computational protein model that equates functionality with binding and catalysis. In the model, marginal stability is not required for ligand-binding functionality and we observe no competing design pressures. The resulting proteins are marginally stable, again demonstrating that neutral evolution is sufficient for explaining marginal stability in observed proteins

Lateral Resistance of Ring-shank Nail Connections in Southern Pine Lumber

Ring-shank nails are used in engineered structures with lateral connection design values based on theoretically derived equations which were validated only for common nails. The goal of this study was to quantify the input parameters and lateral connection strength of several types of ring-shank nails in Southern Pine lumber and critically evaluate the applicability of the theoretical equations for ring-shank nails. Two sizes of galvanized and ungalvanized, hardened steel ring-shank nails from two manufacturers were studied. The hardened, ring-shank nails carried significantly higher loads than the common wire nails studied. Because the current method of determining yield load does not give adequate credit to hardened, ring-shank nails, an alternate method is proposed

Assessing the Accuracy of Ancestral Protein Reconstruction Methods

The phylogenetic inference of ancestral protein sequences is a powerful technique for the study of molecular evolution, but any conclusions drawn from such studies are only as good as the accuracy of the reconstruction method. Every inference method leads to errors in the ancestral protein sequence, resulting in potentially misleading estimates of the ancestral protein's properties. To assess the accuracy of ancestral protein reconstruction methods, we performed computational population evolution simulations featuring near-neutral evolution under purifying selection, speciation, and divergence using an off-lattice protein model where fitness depends on the ability to be stable in a specified target structure. We were thus able to compare the thermodynamic properties of the true ancestral sequences with the properties of “ancestral sequences” inferred by maximum parsimony, maximum likelihood, and Bayesian methods. Surprisingly, we found that methods such as maximum parsimony and maximum likelihood that reconstruct a “best guess” amino acid at each position overestimate thermostability, while a Bayesian method that sometimes chooses less-probable residues from the posterior probability distribution does not. Maximum likelihood and maximum parsimony apparently tend to eliminate variants at a position that are slightly detrimental to structural stability simply because such detrimental variants are less frequent. Other properties of ancestral proteins might be similarly overestimated. This suggests that ancestral reconstruction studies require greater care to come to credible conclusions regarding functional evolution. Inferred functional patterns that mimic reconstruction bias should be reevaluated

Clover species cover on summer dry hill country in Central Otago

The prevalence of annual clover species and white clover (Trifolium repens) during the critical late winter to early summer period (mid Aug – Dec) are compared in relation to aspect, altitude, temperature and rainfall on Mt Grand at Hawea Flat. Measurements were at four north facing sites (450, 620, 750, 910 m a.s.l.) and one shady site at 630 m a.s.l. The rainfall was similar for all altitudes and aspects but annual clovers dominated on sunny faces and the perennial white clover dominated on the shady face with suckling (T. dubium) the only adventive annual clover present. Annual cluster clover (T. glomeratum) dominated on the lower sunny faces at 450 and 620 m and sub clover (T. subterraneum) dominated at 750 m. Suckling and striated clover (T. striatum) were present on all sunny aspect sites and were unaffected by altitude while haresfoot (T. arvense) presence increased with altitude. Air thermal time accumulation for the mid Aug-Dec period was 1440 °Cd at the 450 m site and declined at 100 °Cd per 100 m of elevation (r² = 0.99). Thermal time at 910 m was <1000 °Cd and may limit seed production of some annual clover species at or above this altitude. The dominance of adventive annual clovers on the sunny aspects indicates areas that are probably suitable for introduction of improved annual species such as balansa clover (T. michelianum) or modern cultivars of sub. Productivity of perennial white clover which has persisted on the shady faces may be increased by more intensive grazing management

Withdrawal Strength of Ring-shank Nails Embedded in Southern Pine Lumber

Ring-shank nails are used extensively in post-frame construction due to their superior performance, yet surprisingly little testing has been done on nail sizes above 12d. Experience in the post-frame industry suggests that published allowable design values for ring-shank nails may be overly conservative and need revision. The goal of the research reported herein was to characterize the withdrawal strength of ring-shank nails embedded in Southern Pine lumber. Three sizes ofgalvanized and ungalvanized (bright) ring-shank nails from two manufacturers were studied. Ring-shank nails had approximately twice the withdrawal resistance of smooth-shank nails of the same diameter. Galvanizing slightly reduced withdrawal strength (approximately 8%) due to partial filling of the threads. Nail head pull-through was studied as a possible failure mode. Even allowing for galvanizing and head pull-through, strong evidence is presentedfor increasing withdrawal design valuesfor ring-shank nails

Journal flipping: A case study from Metropolitan Universities

Poster presented at IUPUI Research Day, April 8, 2016Recent events in scholarly publishing, such as the editorial board of Elsevier’s Lingua resigning en masse, shed light on the dilemma faced by many journal editors: balancing a desire to increase impact with promoting open and sustainable models for publishing. These two goals are not mutually exclusive. Recently, editors and publishers are seeing success in reconciling these goals by converting subscription-based journals to open-access, through a process commonly called journal flipping. The IUPUI University Library has a history of supporting the publication of open-access scholarly journals through its Open Access Journals at IUPUI program (http://journals.iupui.edu/). A number of titles, most notably Advances in Social Work and Metropolitan Universities, began as subscription-based journals that were only available in print. This poster presents the process for "flipping" Metropolitan Universities, digitizing the full run of issues and making them openly available via IUPUI’s instance of Open Journal Systems

Threaded-nail Fasteners - Research and Standardization Needs

Threaded nail fasteners are commonly used in agricultural and commercial post-frame structures, yet there has been insufficient research to fully understand the effect of threads on withdrawal and lateral load resistance. The objective of this article is to review technical information on threaded nail fasteners and to identify problems facing manufacturers, designers, and users of threaded nail fasteners for engineering applications. Recommendations are given concerning research and standardization needs