Total Synthesis of Neuroprotective Agents, (+)-Lycibarbarine A and (-)-Lycibarbarine B.

We describe the convergent total syntheses of lycibarbarines A and B which are potent neuroprotective agents recently isolated from the fruits of Lycium barbarum. The synthesis highlights the construction of a unique spiro oxazine heterocyclic motif imbedded in these natural products. The synthesis is accomplished from the commercially available 8-hydroxyquinaline and 2-deoxy-d-ribose as key starting materials. The synthesis features a Reimer-Tiemann reaction, selective amine alkylation with a keto tosylate derivative, and spiroketalization to form an oxazine core.

Evolution reinforces cooperation with the emergence of self-recognition mechanisms: An empirical study of strategies in the Moran process for the iterated prisoner's dilemma.

We present insights and empirical results from an extensive numerical study of the evolutionary dynamics of the iterated prisoner's dilemma. Fixation probabilities for Moran processes are obtained for all pairs of 164 different strategies including classics such as TitForTat, zero determinant strategies, and many more sophisticated strategies. Players with long memories and sophisticated behaviours outperform many strategies that perform well in a two player setting. Moreover we introduce several strategies trained with evolutionary algorithms to excel at the Moran process. These strategies are excellent invaders and resistors of invasion and in some cases naturally evolve handshaking mechanisms to resist invasion. The best invaders were those trained to maximize total payoff while the best resistors invoke handshake mechanisms. This suggests that while maximizing individual payoff can lead to the evolution of cooperation through invasion, the relatively weak invasion resistance of payoff maximizing strategies are not as evolutionarily stable as strategies employing handshake mechanisms.

Entropic Equilibria Selection of Stationary Extrema in Finite Populations.

We propose the entropy of random Markov trajectories originating and terminating at the same state as a measure of the stability of a state of a Markov process. These entropies can be computed in terms of the entropy rates and stationary distributions of Markov processes. We apply this definition of stability to local maxima and minima of the stationary distribution of the Moran process with mutation and show that variations in population size, mutation rate, and strength of selection all affect the stability of the stationary extrema.

Reinforcement learning produces dominant strategies for the Iterated Prisoner's Dilemma.

We present tournament results and several powerful strategies for the Iterated Prisoner's Dilemma created using reinforcement learning techniques (evolutionary and particle swarm algorithms). These strategies are trained to perform well against a corpus of over 170 distinct opponents, including many well-known and classic strategies. All the trained strategies win standard tournaments against the total collection of other opponents. The trained strategies and one particular human made designed strategy are the top performers in noisy tournaments also.

An experimental platform using human intestinal epithelial cell lines to differentiate between hazardous and non-hazardous proteins.

Human intestinal epithelial cell lines (T84, Caco-2, and HCT-8) grown on permeable Transwell™ filters serve as models of the gastrointestinal barrier. In this study, this in vitro model system was evaluated for effectiveness at distinguishing between hazardous and non-hazardous proteins. Indicators of cytotoxicity (LDH release, MTT conversion), monolayer barrier integrity ([(3)H]-inulin flux, horseradish peroxidase flux, trans-epithelial electrical resistance [TEER]), and inflammation (IL-8, IL-6 release) were monitored following exposure to hazardous or non-hazardous proteins. The hazardous proteins examined include streptolysin O (from Streptococcus pyogenes), Clostridium difficile Toxins A and B, heat-labile toxin from enterotoxigenic Escherichia coli, listeriolysin O (from Listeria monocytogenes), melittin (from bee venom), and mastoparan (from wasp venom). Non-hazardous proteins included bovine and porcine serum albumin, bovine fibronectin, and ribulose bisphosphate carboxylase/oxygenase (RuBisco) from spinach. Food allergenic proteins bovine milk ß-lactoglobulin and peanut Ara h 2 were also tested as was the anti-nutritive food protein wheat germ agglutinin. Results demonstrated that this model system effectively distinguished between hazardous and non-hazardous proteins through combined analysis of multiple cells lines and assays. This experimental strategy may represent a useful adjunct to multi-component analysis of proteins with unknown hazard profiles.

The art of war: beyond memory-one strategies in population games.

We show that the history of play in a population game contains exploitable information that can be successfully used by sophisticated strategies to defeat memory-one opponents, including zero determinant strategies. The history allows a player to label opponents by their strategies, enabling a player to determine the population distribution and to act differentially based on the opponent's strategy in each pairwise interaction. For the Prisoner's Dilemma, these advantages lead to the natural formation of cooperative coalitions among similarly behaving players and eventually to unilateral defection against opposing player types. We show analytically and empirically that optimal play in population games depends strongly on the population distribution. For example, the optimal strategy for a minority player type against a resident TFT population is ALLC, while for a majority player type the optimal strategy versus TFT players is ALLD. Such behaviors are not accessible to memory-one strategies. Drawing inspiration from Sun Tzu's the Art of War, we implemented a non-memory-one strategy for population games based on techniques from machine learning and statistical inference that can exploit the history of play in this manner. Via simulation we find that this strategy is essentially uninvadable and can successfully invade (significantly more likely than a neutral mutant) essentially all known memory-one strategies for the Prisoner's Dilemma, including ALLC (always cooperate), ALLD (always defect), tit-for-tat (TFT), win-stay-lose-shift (WSLS), and zero determinant (ZD) strategies, including extortionate and generous strategies.

Inherent randomness of evolving populations.

The entropy rates of the Wright-Fisher process, the Moran process, and generalizations are computed and used to compare these processes and their dependence on standard evolutionary parameters. Entropy rates are measures of the variation dependent on both short-run and long-run behaviors and allow the relationships between mutation, selection, and population size to be examined. Bounds for the entropy rate are given for the Moran process (independent of population size) and for the Wright-Fisher process (bounded for fixed population size). A generational Moran process is also presented for comparison to the Wright-Fisher Process. Results include analytic results and computational extensions.

Comprehensive detection of genes causing a phenotype using phenotype sequencing and pathway analysis.

Discovering all the genetic causes of a phenotype is an important goal in functional genomics. We combine an experimental design for detecting independent genetic causes of a phenotype with a high-throughput sequencing analysis that maximizes sensitivity for comprehensively identifying them. Testing this approach on a set of 24 mutant strains generated for a metabolic phenotype with many known genetic causes, we show that this pathway-based phenotype sequencing analysis greatly improves sensitivity of detection compared with previous methods, and reveals a wide range of pathways that can cause this phenotype. We demonstrate our approach on a metabolic re-engineering phenotype, the PEP/OAA metabolic node in E. coli, which is crucial to a substantial number of metabolic pathways and under renewed interest for biofuel research. Out of 2157 mutations in these strains, pathway-phenoseq discriminated just five gene groups (12 genes) as statistically significant causes of the phenotype. Experimentally, these five gene groups, and the next two high-scoring pathway-phenoseq groups, either have a clear connection to the PEP metabolite level or offer an alternative path of producing oxaloacetate (OAA), and thus clearly explain the phenotype. These high-scoring gene groups also show strong evidence of positive selection pressure, compared with strictly neutral selection in the rest of the genome.

Characteristics and safety assessment of intractable proteins in genetically modified crops.

Genetically modified (GM) crops may contain newly expressed proteins that are described as "intractable". Safety assessment of these proteins may require some adaptations to the current assessment procedures. Intractable proteins are defined here as those proteins with properties that make it extremely difficult or impossible with current methods to express in heterologous systems; isolate, purify, or concentrate; quantify (due to low levels); demonstrate biological activity; or prove equivalency with plant proteins. Five classes of intractable proteins are discussed here: (1) membrane proteins, (2) signaling proteins, (3) transcription factors, (4) N-glycosylated proteins, and (5) resistance proteins (R-proteins, plant pathogen recognition proteins that activate innate immune responses). While the basic tiered weight-of-evidence approach for assessing the safety of GM crops proposed by the International Life Sciences Institute (ILSI) in 2008 is applicable to intractable proteins, new or modified methods may be required. For example, the first two steps in Tier I (hazard identification) analysis, gathering of applicable history of safe use (HOSU) information and bioinformatics analysis, do not require protein isolation. The extremely low level of expression of most intractable proteins should be taken into account while assessing safety of the intractable protein in GM crops. If Tier II (hazard characterization) analyses requiring animal feeding are judged to be necessary, alternatives to feeding high doses of pure protein may be needed. These alternatives are discussed here.

Genome-wide analysis of mutagenesis bias and context sensitivity of N-methyl-N'-nitro-N-nitrosoguanidine (NTG).

We have analyzed the mutation spectrum of N-methyl-N'-nitro-N-nitrosoguanidine (NTG) from a set of 4099 mutations identified from whole-genome sequencing of 32 E. coli strains mutagenized with NTG. These data permit precise measurement of NTG's bias for G/C to A/T transitions (96.6% of all mutations) and also show that NTG mutagenesis is strongly sensitive to context, favoring guanine residues preceded by purines by five-fold over those preceded by pyrimidines. These data give confident estimates for the GC bias and transition/transversion ratios of NTG mutagenesis, which could not be estimated confidently from previous, much smaller datasets.

E. coli Lipopolysaccharide: acute oral toxicity study in mice.

A single dose of endotoxin (lipopolysaccharide) from a common laboratory cloning and expression strain (Escherichia coli BL21[DE3]) was administered to groups of male and female CD-1 mice (n=5/group) at doses up to 1,000,000 endotoxin units (EU) per mouse by oral gavage. The mice were observed for mortality, body weight effects, and clinical signs for 14 days after which they were sacrificed for gross organ necropsy. All mice survived until the scheduled sacrifice, no clinical signs of toxicity were observed, no test substance-related body weight losses occurred and no gross lesions were present at necropsy. Under the conditions of this study, oral administration of E. coli BL21(DE3) endotoxin to mice at a dose of up to 1,000,000 EU/mouse produced no evidence of toxicity.

Phenotype sequencing: identifying the genes that cause a phenotype directly from pooled sequencing of independent mutants.

Random mutagenesis and phenotype screening provide a powerful method for dissecting microbial functions, but their results can be laborious to analyze experimentally. Each mutant strain may contain 50-100 random mutations, necessitating extensive functional experiments to determine which one causes the selected phenotype. To solve this problem, we propose a "Phenotype Sequencing" approach in which genes causing the phenotype can be identified directly from sequencing of multiple independent mutants. We developed a new computational analysis method showing that 1. causal genes can be identified with high probability from even a modest number of mutant genomes; 2. costs can be cut many-fold compared with a conventional genome sequencing approach via an optimized strategy of library-pooling (multiple strains per library) and tag-pooling (multiple tagged libraries per sequencing lane). We have performed extensive validation experiments on a set of E. coli mutants with increased isobutanol biofuel tolerance. We generated a range of sequencing experiments varying from 3 to 32 mutant strains, with pooling on 1 to 3 sequencing lanes. Our statistical analysis of these data (4099 mutations from 32 mutant genomes) successfully identified 3 genes (acrB, marC, acrA) that have been independently validated as causing this experimental phenotype. It must be emphasized that our approach reduces mutant sequencing costs enormously. Whereas a conventional genome sequencing experiment would have cost $7,200 in reagents alone, our Phenotype Sequencing design yielded the same information value for only $1200. In fact, our smallest experiments reliably identified acrB and marC at a cost of only $110-$340.

Toxicology studies with N-acetylglycine.

N-acetylglycine (NAGly) has been identified as a minor constituent of numerous foods. The current paper reports the outcome of in vitro and in vivo genotoxicity, acute oral and repeated dose dietary toxicology studies conducted with NAGly. No evidence of genotoxicity was observed with NAGly in vitro bacterial tester strains or in vivo bone marrow micronucleus studies conducted in mice. No mortalities or evidence of adverse effects were observed in Sprague-Dawley rats following acute oral gavage with NAGly at a dose of 2000 mg/kg of body weight or following repeated dose dietary exposure to NAGly at targeted doses of 100, 500, or 1000 mg/kg of body weight/day for 28 days. No biologically significant or test substance related differences were observed in body weights, feed consumption, or clinical pathology response variables in any of the treatment groups. Based on these results it was concluded that NAGly is not genotoxic or acutely toxic. Further, the no-observed adverse-effect-level (NOAEL) for systemic toxicity from repeated dose dietary exposure to NAGly was 898.9 mg/kg of body weight/day for male rats and 989.9 mg/kg of body weight/day for female rats.

N-acetyl-glutamic acid: evaluation of acute and 28-day repeated dose oral toxicity and genotoxicity.

N-acetyl-glutamic acid (NAG) is an endogenously produced mammalian substance and minor constituent of commonly consumed foods. This paper reports the outcome of genotoxicity and acute and repeated dose (28-day) oral toxicology studies conducted with NAG. No evidence of genotoxicity was observed with NAG in in vitro or in vivo studies. No mortalities or evidence of adverse effects was observed in Sprague-Dawley rats following acute oral gavage with NAG at a dose of 2000 mg/kg of body weight. No adverse effects were observed in rats following repeated dose dietary exposure to NAG at target concentrations corresponding to doses of 100, 500, or 1000 mg/kg of body weight/day for 28 days. All rats survived until scheduled sacrifice and no biologically significant or test substance related differences were observed in body weights, feed consumption, clinical signs, functional observational battery (FOB), ophthalmology, hematology, coagulation, clinical chemistry, organ weights or histopathology of any of the treatment groups. Based on the observed results it is concluded that NAG is not genotoxic or acutely toxic. The no-observed-adverse-effect-level (NOAEL) for systemic toxicity from repeated dose (28-day) dietary exposure to NAG was 914 mg/kg of body weight/day for male rats and 1007 mg/kg of body weight/day for female rats.

Thirteen week feeding study with transgenic maize grain containing event DAS-Ø15Ø7-1 in Sprague-Dawley rats.

Maize line 1507, containing event DAS-Ø15Ø7-1 (1507), is a genetically modified (GM) maize plant that expresses the cry1F gene from Bacillus thuringiensis (Bt) sbsp. aizawai and the phosphinothricin-N-acetyltransferase (pat) gene from Streptomyces viridochromogenes throughout the plant including in the grain expression of the Cry1F protein confers in planta resistance to the European corn borer (ECB; Ostrinia nubilalis Hübner: Crambidae) and other lepidopteran pests. Expression of the PAT protein confers tolerance to the herbicidal active ingredient glufosinate-ammonium. The current study evaluated the nutritional performance of rats fed diets containing 1507 maize grain in a subchronic rodent feeding study. The grains in this study, 1507, its near-isogenic control (33P66), and a non-GM commercial hybrid (33J56) contained similar amounts of proximates, amino acids, minerals, anti-nutrients, and secondary metabolites. The subchronic feeding study compared standard toxicology response variables in rats fed diets containing 1507 maize grain with those in rats fed diets containing non-GM maize grains. All diets were prepared according to the specifications of PMI Nutrition International, LLC Certified Rodent LabDiet 5002 (PMI) 5002). Diets were fed ad libitum to Sprague-Dawley rats for approximately 90 days. In-life response variables included indicators of dietary performance and weekly evaluations for clinical signs of toxicity. No toxicologically significant differences were observed in the nutritional performance variables, clinical and neurobehavioral signs, ophthalmology, clinical pathology (hematology, clinical chemistry, coagulation, and urinalysis), organ weights, and gross and microscopic pathology between any pair of treatment groups. These results demonstrate that 1507 maize grain is as safe and as nutritious as non-GM maize grain.