Practical and predictive bioinformatics methods for the identification of potentially cross-reactive protein matches

A bioinformatics comparison of proteins introduced into food crops through genetic engineering provides a mechanism to identify those proteins that may present an increased risk of allergic reactions for individuals with existing allergies. The goal is to identify proteins that are known to be allergens or are so similar to an allergen that they may induce allergic cross-reactions. Three comparative approaches have traditionally been used, or considered for safety evaluations. One identifies any short (6–8) amino acid segment of the protein that exactly matches a known allergen sequence. The second is an overall primary sequence comparison using Basic Local Alignment Search Tool (BLAST) or FASTA to find matches of greater than 35% identity over 80 amino acids. The third is based on 3-D prediction programs to identify 3-D similarities that might predict potential cross-reactivity. The utility of each of these approaches was debated in the bioinformatics workshop. The consensus agreement from the expert workshop participants was that the short-segment match (e.g., 6–8 amino acids) provides an unacceptably high rate of false positive matches and an uncertain rate of true positive matches, and was not particularly useful for an allergenicity evaluation performed in the context of comprehensive safety evaluation. There was no consensus regarding the most appropriate bioinformatics method, an acceptable scoring criteria for triggering closer examination subsequent to a positive match, or an acceptable scoring mechanism for ranking the utility of the various 3-D approaches that were discussed during the workshop. However, the general consensus was that the most practical approach at this time is to evaluate primary sequence identities to known allergens using either FASTA or BLAST. While there was good agreement that identities of greater than 35% over 80 or more amino acids (recommended by Codex in 2003) is quite conservative, the conclusion was that additional data or studies would be needed to justify changing this criterion as there is some evidence that some individuals sensitized to proteins in evolutionarily conserved protein families may experience cross-reactions to proteins sharing approximately 40% identity

Proof of Grünbaum's conjecture on the stretchability of certain arrangements of pseudolines

AbstractWe prove Grünbaum's conjecture that every arrangement of eight pseudolines in the projective plane is stretchable, i.e., determines a cell complex isomorphic to one determined by an arrangement of lines. The proof uses our previous results on ordered duality in the projective plane and on periodic sequences of permutations of [1,n] associated to arrangements of n lines in the euclidean plane

On the combinatorial classification of nondegenerate configurations in the plane

AbstractWe classify nondegenerate plane configurations by attaching, to each such configuration of n points, a periodic sequence of permutations of {1, 2, …, n} which satisfies some simple conditions; this classification turns out to be appropriate for questions involving convexity. In 1881 Perrin stated that every sequence satisfying these conditions was the image of some plane configuration. We show that this statement is incorrect by exhibiting a counterexample, for n = 5, and prove that for n ⩽ 5 every sequence essentially distinct from this one is realized geometrically by giving a complete classification of configurations in these cases; there is 1 combinatorial equivalence class for n = 3, 2 for n = 4, and 19 for n = 5. We develop some basic notions of the geometry of “allowable sequences” in the course of proving this classification theorem. Finally, we state some results and an open problem on the realizability question in the general case

Piloting Participatory Arts-Based Methods for Exploring Indonesians’ Experiences in a U.S. Biotechnology Training Program

Science communication faculty and professionals often train scientists about conveying and delivering critical and sometimes controversial scientific information to public audiences. This qualitative case study was situated in a U.S.-based biotechnology training program funded by the United States Department of Agriculture for connecting Indonesian science fellows with university biotechnology scientists and science communication experts. The researchers piloted a participatory arts-based approach for instructing and researching Indonesian scientists’, professionals’, and educators’ learning and experiences in the program. Participatory and arts-based research has the potential to uncover and bring to light participants’ perceptions. Participants used iPad multimedia kits to demonstrate their learning of the training’s science communication content, co-constructed and conducted interviews, and captured photos and videos chronicling their experiences throughout the program. Results showed participants’ photos predominantly focused on field site and laboratory visits during the training and participants effectively applied digital storytelling techniques presented in the workshops. Themes from the co-constructed interviews included participants’ definitions of biotechnology, concerns about regulation, labeling, and public understanding, and expressing a hope that biotechnology may improve food security in Indonesia. This pilot study has implications for future international science communication training via intentional instructional design and arts-based research for a culture-centered communication approach

Stopping Light on a Defect

Gap solitons are localized nonlinear coherent states which have been shown both theoretically and experimentally to propagate in periodic structures. Although theory allows for their propagation at any speed $v$, $0\le v\le c$, they have been observed in experiments at speeds of approximately 50% of $c$. It is of scientific and technological interest to trap gap solitons. We first introduce an explicit multiparameter family of periodic structures with localized defects, which support linear defect modes. These linear defect modes are shown to persist into the nonlinear regime, as {\it nonlinear defect modes}. Using mathematical analysis and numerical simulations we then investigate the capture of an incident gap soliton by these defects. The mechanism of capture of a gap soliton is resonant transfer of its energy to nonlinear defect modes. We introduce a useful bifurcation diagram from which information on the parameter regimes of gap soliton capture, reflection and transmission can be obtained by simple conservation of energy and resonant energy transfer principles.Comment: 45 pages, Submitted to Journal of the Optical Society

Intragenic alternative splicing coordination is essential for Caenorhabditis elegans slo-1 gene function

Alternative splicing is critical for diversifying eukaryotic proteomes, but the rules governing and coordinating splicing events among multiple alternate splice sites within individual genes are not well understood. We developed a quantitative PCR-based strategy to quantify the expression of the 12 transcripts encoded by the Caenorhabditis elegans slo-1 gene, containing three alternate splice sites. Using conditional probability-based models, we show that splicing events are coordinated across these sites. Further, we identify a point mutation in an intron adjacent to one alternate splice site that disrupts alternative splicing at all three sites. This mutation leads to aberrant synaptic transmission at the neuromuscular junction. In a genomic survey, we found that a UAAAUC element disrupted by this mutation is enriched in introns flanking alternate exons in genes with multiple alternate splice sites. These results establish that proper coordination of intragenic alternative splicing is essential for normal physiology of slo-1 in vivo and identify putative specialized cis-regulatory elements that regulate the coordination of intragenic alternative splicing

Coherent Backscattering of Ultracold Atoms

We report on the direct observation of coherent backscattering (CBS) of ultracold atoms, in a quasi-two-dimensional configuration. Launching atoms with a well-defined momentum in a laser speckle disordered potential, we follow the progressive build up of the momentum scattering pattern, consisting of a ring associated with multiple elastic scattering, and the CBS peak in the backward direction. Monitoring the depletion of the initial momentum component and the formation of the angular ring profile allows us to determine microscopic transport quantities. The time resolved evolution of the CBS peak is studied and is found a fair agreement with predictions, at long times as well as at short times. The observation of CBS can be considered a direct signature of coherence in quantum transport of particles in disordered media. It is responsible for the so called weak localization phenomenon, which is the precursor of Anderson localization.Comment: 5 pages, 4 figure

Wild Buckwheat Is Unlikely to Pose a Risk to Buckwheat-Allergic Individuals

Buckwheat (Fagopyrum esculentum) is a commonly allergenic food especially in Asia where buckwheat is more commonly consumed. Wild buckwheat (Polygonum convolvulus, recently changed to Fallopia convolvulus) is an annual weed prevalent in grain-growing areas of the United States. Wild buckwheat is not closely related to edible buckwheat although the seeds do have some physical resemblance. A large shipment of wheat into Japan was halted by the discovery of the adventitious presence of wild buckwheat seeds over possible concerns for buckwheat-allergic consumers. However, IgE-binding was not observed to an extract of wild buckwheat using sera from 3 buckwheat-allergic individuals either by radio-allergosorbent test inhibition or by immunoblotting after protein separation by sodium dodecyl sulfate–polyacrylamide gel electrophoresis. Furthermore, the extract of wild buckwheat was not detected in a buckwheat enzyme-linked immunosorbent assay developed with antisera against common buckwheat. Thus, wild buckwheat is highly unlikely to pose any risk to buckwheat-allergic individuals. The common names of plants should not be a factor in the risk assessment for possible cross-allergenicity

Challenges in Gluten Analysis: A Comparison of Four Commercial Sandwich ELISA Kits

Gluten is composed of prolamin and glutelin proteins from several related grains. Because these proteins are not present in identical ratios in the various grains and because they have some differences in sequence, the ability to accurately quantify the overall amount of gluten in various food matrices to support gluten-free labeling is difficult. Four sandwich ELISAs (the R-Biopharm AG R5 RIDASCREEN®, the Neogen Veratox® R5, the Romer Labs AgraQuant® G12, and the Morinaga Wheat kits) were evaluated for their performance to quantify gluten concentrations in various foods and ingredients. The Morinaga and AgraQuant® G12 tests yielded results comparable to the two R5 kits for most, but not for certain, foods. The results obtained with the Morinaga kit were lower when compared to the other kits for analyzing powders of buckwheat and several grass-based products. All four kits were capable of detecting multiple gluten-containing grain sources including wheat, rye, barley, semolina, triticale, spelt, emmer, einkorn, Kamut™, and club wheat. Users of the ELISA kits should verify the performance in their hands, with matrices that are typical for their specific uses. The variation in results for some food matrices between test methods could result in trade disputes or regulatory disagreements