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

Twenty-eight years of GM Food and feed without harm: why not accept them?

Since the first genetically engineered or modified crops or organisms (GMO) were approved for commercial production in 1995, no new GMO has been proven to be a hazard or cause harm to human consumers. These modifications have improved crop efficiency, reduced losses to insect pests, reduced losses to viral and microbial plant pathogens and improved drought tolerance. A few have focused on nutritional improvements producing beta carotene in Golden Rice. Regulators in the United States and countries signing the CODEX Alimentarius and Cartagena Biosafety agreements have evaluated human and animal food safety considering potential risks of allergenicity, toxicity, nutritional and anti-nutritional risks. They consider risks for non-target organisms and the environment. There are no cases where post-market surveillance has uncovered harm to consumers or the environment including potential transfer of DNA from the GMO to nontarget organisms. In fact, many GMOs have helped improve production, yield and reduced risks from chemical insecticides or fungicides. Yet there are generic calls to label foods containing any genetic modification as a GMO and refusing to allow GM events to be labeled as organic. Many African countries have accepted the Cartagena Protocol as a tool to keep GM events out of their countries while facing food insecurity. The rationale for those restrictions are not rational. Other issues related to genetic diversity, seed production and environmental safety must be addressed. What can be done to increase acceptance of safe and nutritious foods as the population increases, land for cultivation is reduced and energy costs soar

Twenty-eight years of GM Food and feed without harm: why not accept them?

Since the first genetically engineered or modified crops or organisms (GMO) were approved for commercial production in 1995, no new GMO has been proven to be a hazard or cause harm to human consumers. These modifications have improved crop efficiency, reduced losses to insect pests, reduced losses to viral and microbial plant pathogens and improved drought tolerance. A few have focused on nutritional improvements producing beta carotene in Golden Rice. Regulators in the United States and countries signing the CODEX Alimentarius and Cartagena Biosafety agreements have evaluated human and animal food safety considering potential risks of allergenicity, toxicity, nutritional and anti-nutritional risks. They consider risks for non-target organisms and the environment. There are no cases where post-market surveillance has uncovered harm to consumers or the environment including potential transfer of DNA from the GMO to nontarget organisms. In fact, many GMOs have helped improve production, yield and reduced risks from chemical insecticides or fungicides. Yet there are generic calls to label foods containing any genetic modification as a GMO and refusing to allow GM events to be labeled as organic. Many African countries have accepted the Cartagena Protocol as a tool to keep GM events out of their countries while facing food insecurity. The rationale for those restrictions are not rational. Other issues related to genetic diversity, seed production and environmental safety must be addressed. What can be done to increase acceptance of safe and nutritious foods as the population increases, land for cultivation is reduced and energy costs soar

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