Rapid Fine Conformational Epitope Mapping Using Comprehensive Mutagenesis and Deep Sequencing

Knowledge of the fine location of neutralizing and non-neutralizing epitopes on human pathogens affords a better understanding of the structural basis of antibody efficacy, which will expedite rational design of vaccines, prophylactics, and therapeutics. However, full utilization of the wealth of information from single cell techniques and antibody repertoire sequencing awaits the development of a high throughput, inexpensive method to map the conformational epitopes for antibody-antigen interactions. Here we show such an approach that combines comprehensive mutagenesis, cell surface display, and DNA deep sequencing. We develop analytical equations to identify epitope positions and show the method effectiveness by mapping the fine epitope for different antibodies targeting TNF, pertussis toxin, and the cancer target TROP2. In all three cases, the experimentally determined conformational epitope was consistent with previous experimental datasets, confirming the reliability of the experimental pipeline. Once the comprehensive library is generated, fine conformational epitope maps can be prepared at a rate of four per day.     

Stimulation of Chromosomal Rearrangements by Ribonucleotides

We show by whole genome sequence analysis that loss of RNase H2 activity increases loss of heterozygosity (LOH) in Saccharomyces cerevisiae diploid strains harboring the pol2-M644G allele encoding a mutant version of DNA polymerase ε that increases ribonucleotide incorporation. This led us to analyze the effects of loss of RNase H2 on LOH and on nonallelic homologous recombination (NAHR) in mutant diploid strains with deletions of genes encoding RNase H2 subunits (rnh201Δ, rnh202Δ, and rnh203Δ), topoisomerase 1 (TOP1Δ), and/or carrying mutant alleles of DNA polymerases ε, α, and δ. We observed an ∼7-fold elevation of the LOH rate in RNase H2 mutants encoding wild-type DNA polymerases. Strains carrying the pol2-M644G allele displayed a 7-fold elevation in the LOH rate, and synergistic 23-fold elevation in combination with rnh201Δ. In comparison, strains carrying the pol2-M644L mutation that decreases ribonucleotide incorporation displayed lower LOH rates. The LOH rate was not elevated in strains carrying the pol1-L868M or pol3-L612M alleles that result in increased incorporation of ribonucleotides during DNA synthesis by polymerases α and δ, respectively. A similar trend was observed in an NAHR assay, albeit with smaller phenotypic differentials. The ribonucleotide-mediated increases in the LOH and NAHR rates were strongly dependent on TOP1. These data add to recent reports on the asymmetric mutagenicity of ribonucleotides caused by topoisomerase 1 processing of ribonucleotides incorporated during DNA replication.     

Polarized Growth of Fungal Hyphae Is Defined by an Alkaline pH Gradient

Robson, G. D., Prebble, E., Rickers, A., Hosking, S., Denning, D. W., Trinci, A. P. J., and Robertson, W. 1996. Polarized growth of fungal hyphae is defined by an alkaline pH gradient. Fungal Genetics and Biology 20, 289-298. Polarized cell growth is exhibited by a diverse range of eukaryotic and prokaryotic cells. The events which are responsible for this growth are poorly understood. However, the existence of ion gradients may play an important role in establishing and driving cell polarity. Using a pH-sensitive, ratiometric fluorescent dye to monitor intracellular pH in growing fungal hyphae, we report a gradient at the extending hyphal tip that is up to 1.4 pH units more alkaline than more distal regions. Both the magnitude and the length of the pH gradient were strongly correlated with the rate of hyphal extension and eradication of the gradient-arrested growth. These results suggest that alkaline pH gradients may be integral to hyphal extension in fungi.     

Isometric force development, isotonic shortening, and elasticity measurements from Ca(2+)-activated ventricular muscle of the guinea pig

Isometric tension and isotonic shortening were measured at constant levels of calcium activation of varying magnitude in mechanically disrupted EGTA-treated ventricular bundles from guinea pigs. The results were as follows: (a) The effect of creatine phosphate (CP) on peak tension and rate of shortening saturated at a CP concentration more than 10 mM; below that level tension was increased and shortening velocity decreased. We interpreted this to mean that CP above 10 mM was sufficient to buffer MgATP(2-) intracellularly. (b) The activated bundles exhibited an exponential stress-strain relationship and the series elastic properties did not vary appreciably with degree of activation or creatine phosphate level. (c) At a muscle length 20 percent beyond just taut, peak tension increased with Ca(2+) concentration over the range slightly below 10(-6) to slightly above 10(-4)M. (d) By releasing the muscle length-active tension curves were constructed. Force declined to 20 percent peak tension with a decrease in muscle length (after the recoil) of only 11 percent at 10(-4)M Ca(2+) and 6 percent at 4x10(-6)M Ca(2+). (e) The rate of shortening after a release was greater at lower loads. At identical loads (relative to maximum force at a given Ca(2+) level), velocity at a given time after the release was less at lower Ca(2+) concentrations; at 10 M(-5), velocity was 72 percent of that at 10(-4)M, and at 4x10(-6)M, active shortening was usually delayed and was 40 percent of the velocity at 10(-4) M. Thus, under the conditions of these experiments, both velocity and peak tension depend on the level of Ca(2+) activation over a similar range of Ca(2+) concentration.     

Quantifying anthropogenic wolf mortality in relation to hunting regulations and landscape attributes across North America

Understanding the types and magnitude of human‐caused mortality is essential for maintaining viable large carnivore populations. We used a database of cause‐specific mortality to examine how hunting regulations and landscape configurations influenced human‐caused mortality of North American gray wolves (Canis lupus). Our dataset included 21 studies that monitored the fates of 3564 wolves and reported 1442 mortalities. Human‐caused mortality accounted for 61% of mortality overall, with 23% due to illegal harvest, 16% due to legal harvest, and 12% the result of management removal. The overall proportion of anthropogenic wolf mortality was lowest in areas with an open hunting season compared to areas with a closed hunting season or mixed hunting regulations, suggesting that harvest mortality was neither fully additive nor compensatory. Proportion of mortality from management removal was reduced in areas with an open hunting season, suggesting that legal harvest may reduce human‐wolf conflicts or alternatively that areas with legal harvest have less potential for management removals (e.g., less livestock depredation). Proportion of natural habitat was negatively correlated with the proportion of anthropogenic and illegal harvest mortality. Additionally, the proportion of mortality due to illegal harvest increased with greater natural habitat fragmentation. The observed association between large patches of natural habitat and reductions in several sources of anthropogenic wolf mortality reiterate the importance of habitat preservation to maintain wolf populations. Furthermore, effective management of wolf populations via implementation of harvest may reduce conflict with humans. Effective wolf conservation will depend on holistic strategies that integrate ecological and socioeconomic factors to facilitate their long‐term coexistence with humans.     

Correlation of chitosan's rheological properties and its ability to electrospin

Chitosan-based, defect-free nanofibers with average diameters ranging from 62 +/- 9 nm to 129 +/- 16 nm were fabricated via electrospinning blended solutions of chitosan and polyethylene oxide (PEO). Several solution parameters such as acetic acid concentration, polymer concentration, and polymer molecular weight were investigated to optimize fiber consistency and diameter. These parameters were evaluated using the rheological properties of the solutions as well as images produced by scanning electron microscopy (SEM) of the electrospun nanofibers. Generally, SEM imaging demonstrated that as total polymer concentration (chitosan + PEO) increased, the number of beads decreased, and as chitosan concentration increased, fiber diameter decreased. Chitosan-PEO solutions phase separate over time; as a result, blended solutions were able to be electrospun with the weakest electric field and the least amount of complications when solutions were electrospun within 24 h of initially being blended. The addition of NaCl stabilized these solutions and increased the time the blended solutions could be stored before electrospinning. Pure chitosan nanofibers with high degrees of deacetylation (about 80%) were unable to be produced. When attempting to electrospin highly deacetylated chitosan from aqueous acetic acid at concentrations above the entanglement concentration, the electric field was insufficient to overcome the combined effect of the surface tension and viscosity of the solution. Therefore, the degree of deacetylation is an extremely important parameter to consider when attempting to electrospin chitosan.     

Quantitative multi‐locus metabarcoding and waggle dance interpretation reveal honey bee spring foraging patterns in Midwest agroecosystems

We explored the pollen foraging behaviour of honey bee colonies situated in the corn and soybean dominated agroecosystems of central Ohio over a month‐long period using both pollen metabarcoding and waggle dance inference of spatial foraging patterns. For molecular pollen analysis, we developed simple and cost‐effective laboratory and bioinformatics methods. Targeting four plant barcode loci (ITS2, rbcL, trnL and trnH), we implemented metabarcoding library preparation and dual‐indexing protocols designed to minimize amplification biases and index mistagging events. We constructed comprehensive, curated reference databases for hierarchical taxonomic classification of metabarcoding data and used these databases to train the metaxa 2 DNA sequence classifier. Comparisons between morphological and molecular palynology provide strong support for the quantitative potential of multi‐locus metabarcoding. Results revealed consistent foraging habits between locations and show clear trends in the phenological progression of honey bee spring foraging in these agricultural areas. Our data suggest that three key taxa, woody Rosaceae such as pome fruits and hawthorns, Salix, and Trifolium provided the majority of pollen nutrition during the study. Spatially, these foraging patterns were associated with a significant preference for forests and tree lines relative to herbaceous land cover and nonflowering crop fields.