Cognitive capacities for cooking in chimpanzees

The transition to a cooked diet represents an important shift in human ecology and evolution. Cooking requires a set of sophisticated cognitive abilities, including causal reasoning, self-control and anticipatory planning. Do humans uniquely possess the cognitive capacities needed to cook food? We address whether one of humans'' closest relatives, chimpanzees (Pan troglodytes), possess the domain-general cognitive skills needed to cook. Across nine studies, we show that chimpanzees: (i) prefer cooked foods; (ii) comprehend the transformation of raw food that occurs when cooking, and generalize this causal understanding to new contexts; (iii) will pay temporal costs to acquire cooked foods; (iv) are willing to actively give up possession of raw foods in order to transform them; and (v) can transport raw food as well as save their raw food in anticipation of future opportunities to cook. Together, our results indicate that several of the fundamental psychological abilities necessary to engage in cooking may have been shared with the last common ancestor of apes and humans, predating the control of fire.     

Analysis and prediction of the packing of α-helices against a β-sheet in the tertiary structure of globular proteins

The packing of α-helices and β-sheets in six $\text{α}\text{β}$ proteins (e.g. flavodoxin) has been analysed. The results provide the basis for a computer algorithm to predict the tertiary structure of an $\text{α}\text{β}$ protein from its amino acid sequence and actual assignment of secondary structure.The packing of an individual α-helix against a β-sheet generally involves two adjacent ± 4 rows of non-polar residues on the α-helix at the positions i, i + 4, i + 8, i + 1, i + 5, i + 9. The pattern of interacting β-sheet residues results from the twisted nature of the sheet surface and the attendant rotation of the side-chains. At a more detailed level, four of the α-helical residues (i + 1, i + 4, i + 5 and i + 8) form a diamond that surrounds one particular β-sheet residue, generally isoleucine, leucine or valine. In general, the α-helix sits 10 Å above the sheet and lies parallel to the strand direction.The prediction follows a combinational approach. First, a list of possible β-sheet structures (10⁶ to 10¹⁴) is constructed by the generation of all β-sheet topologies and β-strand alignments. This list is reduced by constraints on topology and the location of non-polar residues to mediate the sheet/helix packing, and then rank-ordered on the extent of hydrogen bonding. This algorithm was uniformly applied to 16 $\text{α}\text{β}$ domains in 13 proteins. For every structure, one member of the reduced list was close to the crystal structure; the root-mean-square deviation between equivalenced C^α atoms averaged 5.6 Å for 100 residues. For the $\text{α}\text{β}$ proteins with pure parallel β-sheets, the total number of structures comparable to or better than the native in terms of hydrogen bonds was between 1 and 148. For proteins with mixed β-sheets, the worst case is glyceraldehyde-3-phosphate dehydrogenase, where as many as 3800 structures would have to be sampled. The evolutionary significance of these results as well as the potential use of a combinatorial approach to the protein folding problem are discussed.     

Earth Ovens (<Emphasis Type="Italic">Píib</Emphasis>) in the Maya Lowlands: Ethnobotanical Data Supporting Early Use

Earth Ovens ( Píib ) in the Maya Lowlands: Ethnobotanical Data Supporting Early Use. Earth oven cooking is very important among the Yucatec Maya. It is used for daily, festive, and ceremonial occasions, contrasting with other Mesoamerican cultures that use this technique sporadically. In this paper we present an ethnobotanical analysis of the use of earth ovens in a Maya community in Yucatan, Mexico, and discuss its possible antiquity, probable reasons for its continuity, and its current and past importance. We found four oven types in daily use as well as in ritual and celebratory contexts. These involve both men and women in a way that favors transmission of traditional knowledge to the next generation and promotes social bonding and ethnic identity. Of the 46 plant species used in their construction or for the dishes cooked in them, 82% are native and produced in traditional agricultural systems: milpa (kool in Maya) maize-bean-squash association and conuco (pach pakal in Maya) based on tubers such as manioc (Manihot esculenta Crantz). Research suggests that this food preparation technology has the same antiquity as its associated agricultural systems (approximately 3400 to 3000 B.C.E.). Earth ovens were probably used to cook roots and meat in the Archaic and then to cook tamales (vegetal-wrapped maize dough) beginning in the Preclassic. Continuity of traditional agricultural and cultural practices has favored preservation of earth ovens.     

Inhibition of phosphate uptake in barley roots by hydroxy-benzoic acids

The influence of 15 hydroxy-benzoic acids upon active inorganic phosphate absorption by barley roots was examined. For each compound an inhibition constant (k_i) was determined, i.e. the concentration of compound required to bring about a 50% inhibition of absorption. The k_i values of the benzoic acids were strongly correlated with their octanol—water partition coefficients and their pK_a values. This suggests that the inhibition of normal membrane functions, brought about by benzoic acids, results from a generalized increase in cell membrane permeability. Salicylate derivatives were generally more inhibitory than would be predicted from their partition coefficients; their pronounced toxicity probably arises from structural impediments to their detoxication.     

A Simple Algorithm for Finding All k-Edge-Connected Components

The problem of finding k-edge-connected components is a fundamental problem in computer science. Given a graph G = (V, E), the problem is to partition the vertex set V into {V ₁, V ₂,…, V _h}, where each V _i is maximized, such that for any two vertices x and y in V _i, there are k edge-disjoint paths connecting them. In this paper, we present an algorithm to solve this problem for all k. The algorithm preprocesses the input graph to construct an Auxiliary Graph to store information concerning edge-connectivity among every vertex pair in O(Fn) time, where F is the time complexity to find the maximum flow between two vertices in graph G and n = ∣V∣. For any value of k, the k-edge-connected components can then be determined by traversing the auxiliary graph in O(n) time. The input graph can be a directed or undirected, simple graph or multigraph. Previous works on this problem mainly focus on fixed value of k.     

Searching and gradualness

Consider the elements of the power set S as the alternatives in a search space. Each element of the set has a value and the goal of a search is to find an element with near-minimum value. If high-valued elements of cardinality i (recall that elements of S are themselves sets) are subsets of high-valued elements of cardinality i + 1, then the search space has a king of gradualness that should facilitate search.A search algorithm might generate a series, S′(1), … S′(k) of samples in S, where all the elements in S′ (i) have cardinality i. I propose a class of search algorithms, where each algorithm A(j) generates S′(i + 1) by emphasizing the j lowest-valued elements in S′(i). I then define search space gradualness and search algorithm performance and formally relate gradualness and performance.     

Concentration equations for the diffusion of a reversibly reacting substance in gel-like media

The concentration of a diffusible substanceA(x, t) in a semi-infinite geometry is studied for the set of reversible reactionsA+B _i ?C _i ;i=1...n, whereB _i andC _i are assumed to be associated with non-diffusible biological structures. Assuming chemical equilibrium prevails throughout for each reaction, it is shown that a single uncoupled partial differential equation is sufficient to specifyA(x, t) and indirectlyB _i (x, t) andC _i (x, t) as well: $$\left[ {1 + \sum\limits_i {\frac{{K_i \beta _i }}{{\left( {1 + K_i A} \right)^2 }}} } \right]\frac{{\partial A}}{{\partial t}} = D_A \frac{{\partial ^2 A}}{{\partial x^2 }}$$ whereK _i is the chemical equilibrium constant of theith reaction, β₁ is concentration of binding sites of theith species (i.e.B _i+C _i) andD _A is the usual diffusion constant forA. Numerical solutions for boundary conditions amenable to the Boltzman transformation are presented and the range of parameters established over which the uniqueness and convergence of the solutions can be proven.     

Antifungal activity of Leuconostoc citreum and Weissella confusa in rice cakes

The antifungal activity of organic acids greatly improves the shelf life of bread and bakery products. However, little is known about the effect of lactic acid fermentation on fungal contamination in rice cakes. Here, we show that lactic acid fermentation in rice dough can greatly retard the growth of three fungal species when present in rice cakes, namely Cladosporium sp. YS1, Neurospora sp. YS3, and Penicillium crustosum YS2. The antifungal activity of the lactic acid bacteria against these fungi was much better than that of 0.3% calcium propionate. We found that organic acids including lactic and acetic acid, which are byproducts of lactic fermentation or can be artificially added, were the main antifungal substances. We also found that some Leuconostoc citreum and Weissella confusa strains could be good starter species for rice dough fermentation. These results imply that these lactic acid bacteria can be applicable to improve the preservation of rice cakes.     

Crack and cook: A simple and quick process for elimination of concanavalin A (Con A) from Canavalia seeds

The most nutritionally important antinutritional factor in the Canavalia seeds is Concanavalin A (Con A) which takes at least 3 h of cooking at 96°C to inactivate. The effect of breaking the seeds into smaller pieces before cooking on the Con A content was investigated. Whole seeds of Canavalia ensiformis (jackbean) and Canavalia ensiformis seeds that were broken into smaller pieces (3–7 parts per seed) were cooked at 96°C for 30, 60, 90 and 120 min, respectively. Some were cooked for 15, 30 and 45 min, respectively, under pressure using household pressure cooker. Con A content of the products was determined by the hemagglutination of rabbit fresh erythrocytes by the extracted protein samples serially diluted in PBS buffer in 96-microwell plates. Hemagglutinating activity was expressed as minimal concentration of protein inducing hemagglutination of cells. Hemagglutinating activity of the cracked beans was completely eliminated within 1 h of ordinary cooking and 15 min of pressure cooking. The cooked materials took 5–6 h of sunshine to dry to 90% dry matter. The hemagglutinating activity of the whole seeds was eliminated in 45 min of pressure cooking but not in 2 h of ordinary cooking. They took 3 days of same sunshine to dry. The crack and cook process (CAC), the name being proposed for the method, is commercially applicable in view of its relative ease of execution.     

Drying of Tribenuron,a Thermosensitive Biochemical

The extension of microwave use in the biochemical industry was explored by drying tribenuron, a thermosensitive biochemical, in a microwave oven and in a thermal vacuum oven. Tribenuron wet cakes, containing a mixture of solvents, methanol and water, were heated at 40 °C in both ovens. Nitrogen purge was used to prevent the decomposition of tribenuron from prolonged heating. Microwave heating dried tribenuron in twenty minutes while the vacuum oven heating required eighteen hours to dry the wet cakes. In addition, the tribenuron quality was maintained under microwave drying, but deteriorated in the thermal vacuum oven. Therefore, microwave technology is more effective in drying tribenuron than conventional vacuum ovens. The results of this study are important for the use of microwave drying on a large scale in biochemical companies.     

An amino acid code for β‐sheet packing structure

To understand the relationship between protein sequence and structure, this work extends the knob‐socket model in an investigation of β‐sheet packing. Over a comprehensive set of β‐sheet folds, the contacts between residues were used to identify packing cliques: sets of residues that all contact each other. These packing cliques were then classified based on size and contact order. From this analysis, the two types of four‐residue packing cliques necessary to describe β‐sheet packing were characterized. Both occur between two adjacent hydrogen bonded β‐strands. First, defining the secondary structure packing within β‐sheets, the combined socket or XY:HG pocket consists of four residues i, i+2 on one strand and j, j+2 on the other. Second, characterizing the tertiary packing between β‐sheets, the knob‐socket XY:H+B consists of a three‐residue XY:H socket (i, i+2 on one strand and j on the other) packed against a knob B residue (residue k distant in sequence). Depending on the packing depth of the knob B residue, two types of knob‐sockets are found: side‐chain and main‐chain sockets. The amino acid composition of the pockets and knob‐sockets reveal the sequence specificity of β‐sheet packing. For β‐sheet formation, the XY:HG pocket clearly shows sequence specificity of amino acids. For tertiary packing, the XY:H+B side‐chain and main‐chain sockets exhibit distinct amino acid preferences at each position. These relationships define an amino acid code for β‐sheet structure and provide an intuitive topological mapping of β‐sheet packing. Proteins 2014; 82:2128–2140. © 2014 Wiley Periodicals, Inc.     

Genomic prediction of dichotomous traits with Bayesian logistic models

Bayesian methods are a popular choice for genomic prediction of genotypic values. The methodology is well established for traits with approximately Gaussian phenotypic distribution. However, numerous important traits are of dichotomous nature and the phenotypic counts observed follow a Binomial distribution. The standard Gaussian generalized linear models (GLM) are not statistically valid for this type of data. Therefore, we implemented Binomial GLM with logit link function for the BayesB and Bayesian GBLUP genomic prediction methods. We compared these models with their standard Gaussian counterparts using two experimental data sets from plant breeding, one on female fertility in wheat and one on haploid induction in maize, as well as a simulated data set. With the aid of the simulated data referring to a bi-parental population of doubled haploid lines, we further investigated the influence of training set size (N), number of independent Bernoulli trials for trait evaluation (n _i ) and genetic architecture of the trait on genomic prediction accuracies and abilities in general and on the relative performance of our models. For BayesB, we in addition implemented finite mixture Binomial GLM to account for overdispersion. We found that prediction accuracies increased with increasing N and n _i . For the simulated and experimental data sets, we found Binomial GLM to be superior to Gaussian models for small n _i , but that for large n _i Gaussian models might be used as ad hoc approximations. We further show with simulated and real data sets that accounting for overdispersion in Binomial data can markedly increase the prediction accuracy.     

Harmonic analysis of Boolean networks: determinative power and perturbations

Consider a large Boolean network with a feed forward structure. Given a probability distribution on the inputs, can one find, possibly small, collections of input nodes that determine the states of most other nodes in the network? To answer this question, a notion that quantifies the determinative power of an input over the states of the nodes in the network is needed. We argue that the mutual information (MI) between a given subset of the inputs X={X₁,...,X_n} of some node i and its associated function f_i(X) quantifies the determinative power of this set of inputs over node i. We compare the determinative power of a set of inputs to the sensitivity to perturbations to these inputs, and find that, maybe surprisingly, an input that has large sensitivity to perturbations does not necessarily have large determinative power. However, for unate functions, which play an important role in genetic regulatory networks, we find a direct relation between MI and sensitivity to perturbations. As an application of our results, we analyze the large-scale regulatory network of Escherichia coli. We identify the most determinative nodes and show that a small subset of those reduces the overall uncertainty of the network state significantly. Furthermore, the network is found to be tolerant to perturbations of its inputs.     

Some theoretical aspects of protein coevolution in the ecosystem “phage-bacteria” II. The deterministic model of microevolution

The deterministic model of microevolutionary dynamics of “phagebacteria” ecosystem is analyzed. Primary (and after all decisive) events that determine the dynamics are direct interactions between bacterial reception and viral adsorption proteins. Structure of the model is that under real parameters of adsorption, lysis and reproduction each separate (ith) stage of microevolution comes to end with total lysis of ith population of bacteria by ith population of phage. It is shown however that in the course of joint microevolution both populations pass over some critical sizes when a new pair of antagonistic strains arises with certainty from mutations. As a result it is easy to visualize and simulate by computer the process of successive fixations of such pairs of mutants. This coevolution is the original example of a locally adaptive but globally undirected process which is characterized also by: (1) constant average rate, (2) neutrality of mutations at the moment of their emergence and during the period of “anticipation” of ecological changes, (3) pure adaptivity of the same mutations at the moment of proper fixation and (4) “intrinsic origin” (from the ecosystem dynamics itself) of selective constraints.     

Killing for the greater good: Action aversion and the emotional inhibition of harm in moral dilemmas

Moral judgment is influenced by both automatic and deliberative processing systems, and moral conflict arises when these systems produce competing intuitions. We investigated the role of emotional arousal in inhibiting harmful action in a behavioral study of utilitarian tradeoffs in a 3D digital simulation of two classic “trolley” scenarios in which participants decided whether to harm one person in order to avert harm to five others. Physiological arousal was measured via skin conductance response in real time. Results showed that physiological arousal is increased in situations in which using personal harm is necessary to achieve a utilitarian outcome relative to when the same outcome can be achieved with impersonal harm, and is linked to a decreased likelihood of engaging in harmful action, though a test of mediation was not statistically significant. In addition, when the use of personal harm was required to save lives, arousal was higher pre-action relative to post-action. Overall, our findings suggest that physiological arousal may be part of an affective system that functions to inhibit harmful action against others.     

Fluctuations and Noise in Kinetic Systems: Application to K+ Channels in the Squid Axon

We consider the equilibrium or steady-state noise power density spectrum in the quantity N = Σ^x_i=0 a_iN_i for an ensemble of independent and equivalent systems each of which can exist in the discrete set of states i = 0, 1, ···, x. N_i is the number of systems of the ensemble in state i and the a_i's are constants. There is a transition rate constant α_ij for an arbitrary transition i → j; the kinetic equations are linear. There are possible applications to enzyme and biochemical kinetics generally, to membrane transport, muscle contraction, binding on macromolecules, etc. In each case, noise measurements would provide information about the kinetic scheme. The particular application considered here is to K⁺ channels or gates (one channel = one system) in the squid axon membrane: a_iK is the K⁺ conductance of a channel in state i and the kinetic scheme is of the Hodgkin-Huxley type (HH). Here we allow an arbitrary set of a_i's. This is a generalization of our treatment of K⁺ channel noise in an earlier paper. The theory is discussed and some calculations made using Fishman's recent experimental results on K⁺ channel noise as a guide. Preliminary indications are that the HH choice of a_i's may be oversimplified and that a₀ 0, a₁ ≠ a₀, a_x ≠ a_x-1. Quite possibly the a_i's increase from a₀ to a_x, though the early a_i's must be relatively small to give the observed induction behavior in g_K(t). An increase in equal steps is unsatisfactory because this is essentially HH with x = 1 (no induction). More refined experiments may modify these tentative conclusions. In any case, it appears from Fishman's work that noise measurements will probably be very useful in distinguishing between rival models of K⁺ channels.     

Genome‐scale metabolic modeling reveals key features of a minimal gene set

Mesoplasma florum, a fast‐growing near‐minimal organism, is a compelling model to explore rational genome designs. Using sequence and structural homology, the set of metabolic functions its genome encodes was identified, allowing the reconstruction of a metabolic network representing ˜ 30% of its protein‐coding genes. Growth medium simplification enabled substrate uptake and product secretion rate quantification which, along with experimental biomass composition, were integrated as species‐specific constraints to produce the functional iJL208 genome‐scale model (GEM) of metabolism. Genome‐wide expression and essentiality datasets as well as growth data on various carbohydrates were used to validate and refine iJL208. Discrepancies between model predictions and observations were mechanistically explained using protein structures and network analysis. iJL208 was also used to propose an in silico reduced genome. Comparing this prediction to the minimal cell JCVI‐syn3.0 and its parent JCVI‐syn1.0 revealed key features of a minimal gene set. iJL208 is a stepping‐stone toward model‐driven whole‐genome engineering.     

Traceability of Amanita fuliginea poisoning using DNA barcoding and UPLC-MS/MS

Amanita fuliginea is a lethal poisonous mushroom found in Japan and southern China. The primary toxins are α-amanitin (α-AMA) and β-amanitin (β-AMA). There is a lack of systematic and comprehensive investigations on the traceability of A. fuliginea poisoning due to technological limitations. This study aimed to examine whether A. fuliginea poisoning incidents could be traced using DNA barcoding and ultraperformance liquid chromatography coupled with triple quadrupole mass spectrometry (UPLC-MS/MS). We collected A. fuliginea specimens and prepared cooked and cooked plus simulated gastric fluid (SGF)-treated samples. We then performed DNA barcoding of internal transcribed spacer regions for species identification and UPLC-MS/MS for toxin level determination. Our results indicate that under the experimental conditions used herein, DNA barcoding can be used for molecular identification of mushroom samples that are cooked and/or cooked plus SGF-treated for less than 30 min; UPLC-MS/MS can be used for toxin analysis of cooked and SGF-treated (0–1440 min) samples. This is the first time that DNA barcoding and UPLC-MS/MS have been combined for studying the toxicological traceability of A. fuliginea using simulated gastric contents or vomit in northern China. Our data provide support for the treatment of clinical mushroom poisoning cases.