Linkage rules for plant-pollinator networks: trait complementarity or exploitation barriers?

Recent attempts to examine the biological processes responsible for the general characteristics of mutualistic networks focus on two types of explanations: nonmatching biological attributes of species that prevent the occurrence of certain interactions (“forbidden links”), arising from trait complementarity in mutualist networks (as compared to barriers to exploitation in antagonistic ones), and random interactions among individuals that are proportional to their abundances in the observed community (“neutrality hypothesis”). We explored the consequences that simple linkage rules based on the first two hypotheses (complementarity of traits versus barriers to exploitation) had on the topology of plant–pollination networks. Independent of the linkage rules used, the inclusion of a small set of traits (two to four) sufficed to account for the complex topological patterns observed in real-world networks. Optimal performance was achieved by a “mixed model” that combined rules that link plants and pollinators whose trait ranges overlap (“complementarity models”) and rules that link pollinators to flowers whose traits are below a pollinator-specific barrier value (“barrier models”). Deterrence of floral parasites (barrier model) is therefore at least as important as increasing pollination efficiency (complementarity model) in the evolutionary shaping of plant–pollinator networks.     

Sexual selection: Another Darwinian process

Why was sexual selection so important to Darwin? And why was it de-emphasized by almost all of Darwin's followers until the second half of the 20th century? These two questions shed light on the complexity of the scientific tradition named “Darwinism”. Darwin's interest in sexual selection was almost as old as his discovery of the principle of natural selection. From the beginning, sexual selection was just another “natural means of selection”, although different from standard “natural selection” in its mechanism. But it took Darwin 30 years to fully develop his theory, from the early notebooks to the 1871 book The Descent of Man, and Selection in Relation to Sex. Although there is a remarkable continuity in his basic ideas about sexual selection, he emphasized increasingly the idea that sexual selection could oppose the action of natural selection and be non adaptive. In time, he also gave more weight to mate choice (especially female choice), giving explicit arguments in favor of psychological notions such as “choice” and “aesthetic sense”. But he also argued that there was no strict demarcation line between natural and sexual selection, a major difficulty of the theory from the beginning. Female choice was the main reason why Alfred Russel Wallace, the co-discoverer of the principle of natural selection, engaged in a major controversy with Darwin about sexual selection. Wallace was suspicious about sexual selection in general, trying to minimize it by all sorts of arguments. And he denied entirely the existence of female choice, because he thought that it was both unnecessary and an anthropomorphic notion. This had something to do with his spiritualist convictions, but also with his conception of natural selection as a sufficient principle for the evolutionary explanation of all biological phenomena (except for the origin of mind). This is why Wallace proposed to redefine Darwinism in a way that excluded Darwin's principle of sexual selection. The main result of the Darwin–Wallace controversy was that most Darwinian biologists avoided the subject of sexual selection until at least the 1950 s, Ronald Fisher being a major exception. This controversy still deserves attention from modern evolutionary biologists, because the modern approach inherits from both Darwin and Wallace. The modern approach tends to present sexual selection as a special aspect of the theory of natural selection, although it also recognizes the big difficulties resulting from the inevitable interaction between these two natural processes of selection. And contra Wallace, it considers mate choice as a major process that deserves a proper evolutionary treatment. The paper's conclusion explains why sexual selection can be taken as a test case for a proper assessment of “Darwinism” as a scientific tradition. Darwin's and Wallace's attitudes towards sexual selection reveal two different interpretations of the principle of natural selection: Wallace's had an environmentalist conception of natural selection, whereas Darwin was primarily sensitive to the element of competition involved in the intimate mechanism of any natural process of selection. Sexual selection, which can lack adaptive significance, reveals this exemplarily.     

Configural processing of different topologically structured figures: an ERP Study

According to Chen’s theory, topological differences are perceived faster than feature differences in early visual perception. We hypothesized that topological perception is caused by the sensitivity in discriminating figures with and without “holes”. An ERP experiment was conducted utilizing a passive paradigm to investigate the differences in perceiving figures with “hole” and with “no-hole”. The results showed differences in N170 components between figures with “holes” and with “no-holes”. The inversion of the “hole” could influence the latency of N170, but the inversion of the “no-hole” could not, which indicated that global features are processed first in the “hole” perception whilst local features are given priority to the “no-hole” perception. This result was similar to studies concerning face and non-face objects, suggesting a configural processing of the “hole”.     

Darwin's apes and “savages”

Since his visit to Tierra del Fuego in the 1830s, Darwin had been fascinated by the “savages” that succeeded in surviving on such a “broken beach”, and because they were certainly similar in behaviour to our ancestors. However, he was also fascinated by baboons’ behaviour, according to Brehm's accounts: hamadryas baboons showed a strong altruism to the point of risking their own lives in order to save their infants from attack by dogs. In 1871, he mentions he would rather have descended from brave baboons than from “savages”, considered egoistic. We study the two sources of these ideas and try to show how Darwin's comparative reflections on apes and “savages” made him the first evolutionist anthropologist.     

Darwin's puzzling Expression

Charles Darwin's The Expression of the Emotions in Man and Animals (1872) is a very different kind of work from On the Origin of Species (1859). This “otherness” is most extreme in the character of the explanations that Darwin offers in the Expression. Far from promoting his theory of natural selection, the Expression barely mentions that theory, instead drawing on explanatory principles which recall less Darwinian than Lamarckian and structuralist biological theorizing. Over the years, historians have offered a range of solutions to the puzzle of why the Expression is so “non-Darwinian”. Close examination shows that none of these meets the case. However, recent research on Darwin's lifelong engagement with the controversies in his day over the unity of the human races makes possible a promising new solution. For Darwin, emotional expression served the cause of defending human unity precisely to the extent that natural selection theory did not apply.     

Darwin teleologist? Design in the Orchids

Focusing on the Orchids, this article aims at disentangling the concepts of teleology, design and natural theology. It refers to several contemporary critics of Darwin (Kölliker, Argyll, Royer, Candolle, Delpino) to challenge Huxley's interpretation that Darwin's system was “a deathblow” to teleology. The Orchids seem rather to be a “flank-movement” (Gray): it departs from the Romantic theories of transmutation and the “imaginary examples” of the Origin; it focuses on empirical data and on teleological structures. Although Darwin refers to natural selection, his readers mock him for his fascination for delicate morphological contrivances and co-adaptations – a sign that he was inescapably lured to finality. Some even suggested that his system was a “theodicy”. In the history of Darwinism, the Orchids reveal “another” quite unexpected and heterodox Darwin: freed from the hypothetical fancies of the Origin, and even suggesting a new kind of physico-theology.     

Expected utility violations evolve under status-based selection mechanisms

The expected utility theory of decision making under uncertainty, a cornerstone of modern economics, assumes that humans linearly weight “utilities” for different possible outcomes by the probabilities with which these outcomes occur. Despite the theory's intuitive appeal, both from normative and from evolutionary perspectives, many experiments demonstrate systematic, though poorly understood, patterns of deviation from EU predictions. This paper offers a novel theoretical account of such patterns of deviation by demonstrating that EU violations can emerge from evolutionary selection when individual “status” affects inclusive fitness. In humans, battles for resources and social standing involve high-stakes decision making, and assortative mating ensures that status matters for fitness outcomes. The paper therefore proposes grounding the study of decision making under uncertainty in an evolutionary game-theoretic framework.     

Comparing two methods of calculating the probability of absence: the Negative Predictive Value, and a Credible Interval

If sampling fails to reveal the presence of an invasive species with potential to actually be present, how may we calculate the probability that it is truly absent, e.g. didymo (Didymosphenia geminate) in New Zealand’s North Island. In statistical terms this is a Bayesian question, concerning the probability of a hypothesis (presence/absence), given the obtained data (all results negative). “Classical” theory doesn’t answer this question, because it inverts the required considerations by calculating the probability of all samples being absent if the invasive was actually present. Accordingly, the Bayesian view of “probability” must be adopted in order to answer the question. That definition differs from classical probability in that it always includes an element of subjective belief, particularly in the choice of an appropriate “prior probability” (this is our belief as to the presence of the invasive organism before collecting new data). Bayesian methods can therefore be somewhat controversial – but we seem forced to use them. One Bayesian approach is to use the “Negative Predictive Value”, in which a point estimate of the probability of presence (or absence) prior to sample collection (the “prior probability”) is updated using data once collected using Bayes’ rule. This is in common use in medical studies, where the prior probability is the background disease prevalence, which is generally well understood. It is sometimes used in environmental ‘hot-spot’ investigations. An alternative approach is to recognise the uncertainty in the prior belief by using a distribution of prior probability and updating that using data once collected to give a Credible Interval in which the probability of presence (or absence) should lie – if all our assumptions have been satisfied. We will compare the merits of these approaches considering didymo, southern salt marsh mosquito (Aedes camptorhychus) and the sea squirt Styela clava.     

Prediction bands and intervals for the scapulo-humeral coordination based on the Bootstrap and two Gaussian methods

Quantitative motion analysis protocols have been developed to assess the coordination between scapula and humerus. However, the application of these protocols to test whether a subject's scapula resting position or pattern of coordination is “normal”, is precluded by the unavailability of reference prediction intervals and bands, respectively. The aim of this study was to present such references for the “ISEO” protocol, by using the non-parametric Bootstrap approach and two parametric Gaussian methods (based on Student's T and Normal distributions).     

Emergence and properties of spice and bath salts: A medicinal chemistry perspective

Over the past five years the number of internet sites advertising “legal highs” has literally exploded, as have user reports of experiences (both pleasurable and frightening) with these substances and the number of emergency room visits by users. Although the majority of these “legal highs” have been described as bath salts and herbal extracts, most contain neither plant derived compounds nor components of personal hygiene products. So-called “bath salts” largely contain synthetic analogs of the natural compound Khat; spice-related materials, claimed to be “legal marijuana,” are mostly synthetic analogs of cannabinoid receptor ligands that were developed as research tools. This review describes the emergence and properties of these two groups of “legal highs” from a medicinal chemist's perspective.     

Melanization in the genus Propithecus Malagasey Lemur

Among the Lemurs of Madagascar the genus Propithecus contributes two species, but these are differentiated into numerous forms (subspecies and intermediates between them) which are essentially characterized by pelage coloration. The existence of certain “melanizing” forms among these intermediates permits us to examine the problem of the evolution of this genus in Madagascar, invoking a hypothesis to explain these chromatic variations. Hershkovitz's theory of “Metachromism” could easily fit the case of Propithecus. It would permit derivation of the light-coloured forms of the north, west and the south from a primitive form close to the dark-coloured Propithecus diadema of the southeast.     

Circadian aspects of body temperature regulation in exercise

Internal and external factors contribute to resting core temperature and affect thermoregulation. Also, a robust circadian rhythm exists, implying that the body is in “heat-gain” or “heat-loss” modes at different times during the 24 h. Moreover, many variables associated with exercise, and the body's capacity for exercise, show circadian variation. All these factors contribute to circadian changes in thermoregulation during exercise. Attention is focused on responses at the onset of exercise, “critical temperature”, and recovery after exercise. Practical implications of circadian changes in thermoregulation during exercise include ergogenic aids and inter-individual differences, including those due to gender, age and acclimatisation.     

Characterization and polymorphism of Keratin Associated Protein 1.4 gene in goats

Keratin-associated proteins (KAPs) are among the main structural components of the animal fibers and form semi-rigid matrix wherein the keratin intermediate filaments (KIFs) are embedded. Variation in the KAP genes has been reported to affect the structure of KAPs and hence fiber characteristics. As no information is available on this gene in Capra hircus therefore, present work was undertaken to characterize and explore the different polymorphic variants of KAP1.4 gene at DNA level in different breeds/genetic groups of goats of Kashmir. Cashmere (Changthangi, 30 animals) and non-Cashmere (Bakerwal and Kargil goats, 20 animals each) goats formed the experimental animals for the study. Single strand conformation polymorphism technique was employed for exploring variability at gene level. On exploring the size variability in KAP1.4 gene between Ovine and Caprine, it was concluded that sheep KAP1.4 gene has a deletion of 30 nucleotides. In comparison to published nucleotide sequences of sheep, goat sequences explored are differing at positions 174, 462 and 568 and at these positions “G”, “T” and “T” nucleotides are present in sheep, but are replaced by “A”, “C” and “C” respectively, in goats. By SSC studies, two genotypes were observed in each genetic group and in Bakerwal goats the genotypes were designated as A1A1 (0.40) and A1A2 (0.60) and were formed by two alleles A1 (0.70) andA2 (0.30). The different SSC patterns observed in Kargil goats were designated as B1B1 (0.35) and B1B2 (0.65) genotypes with frequencies of B1 and B2 alleles as 0.675 and 0.325, respectively. Similarly, two genotypes C1C1 (0.60) and C1C2 (0.40) were observed in Changthangi goats and the frequencies of C1 and C2 alleles were 0.80 and 0.20, respectively. These alleles were later confirmed by sequencing. The sequences of these alleles are available in NCBI under Acc. No's. JN012101.1, JN012102.1, JN000317.1, JN000318.1, JQ436929 and JQ627657. It was concluded that all the alleles observed in a breed were unique to the breed. The designated A1 and A2 alleles of Bakerwal goats differ from each other at positions 245 and the nucleotides observed were “C” or “A” and at position 605 of the nucleotide sequence “T” or “C”, were observed. The designated B1 and B2 alleles of Kargil goats differed from each other at positions 224, 374, 375 and 521. The nucleotides observed in two SSC pattern were C→G, A→G, G→A and T→C, respectively. The designated C1 and C2 alleles of Changthangi goats differed from each other at one position 440 with the change of “A”→“C”.     

Extensive conformational transitions are required to turn on ATP hydrolysis in myosin

Conventional myosin is representative of biomolecular motors in which the hydrolysis of adenosine triphosphate (ATP) is coupled to large-scale structural transitions both in and remote from the active site. The mechanism that underlies such “mechanochemical coupling,” especially the causal relationship between hydrolysis and allosteric structural changes, has remained elusive despite extensive experimental and computational analyses. In this study, using combined quantum mechanical and molecular mechanical simulations and different conformations of the myosin motor domain, we provide evidence to support that regulation of ATP hydrolysis activity is not limited to residues in the immediate environment of the phosphate. Specifically, we illustrate that efficient hydrolysis of ATP depends not only on the proper orientation of the lytic water but also on the structural stability of several nearby residues, especially the Arg238-Glu459 salt bridge (the numbering of residues follows myosin II in Dictyostelium discoideum) and the water molecule that spans this salt bridge and the lytic water. More importantly, by comparing the hydrolysis activities in two motor conformations with very similar active-site (i.e., Switches I and II) configurations, which distinguished this work from our previous study, the results clearly indicate that the ability of these residues to perform crucial electrostatic stabilization relies on the configuration of residues in the nearby N-terminus of the relay helix and the “wedge loop.” Without the structural support from those motifs, residues in a closed active site in the post-rigor motor domain undergo subtle structural variations that lead to consistently higher calculated ATP hydrolysis barriers than in the pre-powerstroke state. In other words, starting from the post-rigor state, turning on the ATPase activity requires not only displacement of Switch II to close the active site but also structural transitions in the N-terminus of the relay helix and the “wedge loop,” which have been proposed previously to be ultimately coupled to the rotation of the converter subdomain 40 Å away.     

The dynamics of collagen uncrimping and lateral contraction in tendon and the effect of ionic concentration

Under tensile loading, tendon undergoes a number of unique structural changes that govern its mechanical response. For example, stretching a tendon is known to induce both the progressive “uncrimping” of wavy collagen fibrils and extensive lateral contraction mediated by fluid flow out of the tissue. However, it is not known whether these processes are interdependent. Moreover, the rate-dependence of collagen uncrimping and its contribution to tendon's viscoelastic mechanical properties are unknown. Therefore, the objective of this study was to (a) develop a methodology allowing for simultaneous measurement of crimp, stress, axial strain and lateral contraction in tendon under dynamic loading; (b) determine the interdependence of collagen uncrimping and lateral contraction by testing tendons in different swelling conditions; and (c) assess how the process of collagen uncrimping depends on loading rate. Murine flexor carpi ulnaris (FCU) tendons in varying ionic environments were dynamically stretched to a set strain level and imaged through a plane polariscope with the polarizer and analyzer at a fixed angle. Analysis of the resulting images allowed for direct measurement of the crimp frequency and indirect measurement of the tendon thickness. Our findings demonstrate that collagen uncrimping and lateral contraction can occur independently and interstitial fluid impacts tendon mechanics directly. Furthermore, tensile stress, transverse contraction and degree of collagen uncrimping were all rate-dependent, suggesting that collagen uncrimping plays a role in tendon's dynamic mechanical response. This study is the first to characterize the time-dependence of collagen uncrimping in tendon, and establishes structure–function relationships for healthy tendons that can be used to better understand and assess changes in tendon mechanics after disease or injury.     

A slowing effect on visual search by advance information in pigeons (Columba livia): a comparison with humans (Homo sapiens)

A comparative study was conducted to investigate whether the search for a target letter was facilitated when the target and prime (preceding stimulus) letters were identical. Pigeons (Section 2) and human participants (Section 3) were first trained to search for “A” among “Y”s and “E” among “D”s in a condition in which a square shape appeared as the prime (Neutral condition). In subsequent testing, a prime was identical either to the corresponding target (Target-priming condition) or to the distractor (Distractor-priming condition). Humans and pigeons responded differently to the two priming conditions. On early trials, the Target prime facilitated search in humans, reducing reaction times (RTs) to targets. In pigeons, however, RTs were longer with Target primes, suggesting that pre-exposure to target letters may directly inhibit the search for targets in subsequent search displays. Furthermore, pre-exposure to the distractor letters may inhibit the processing of the distractor. On later trials, RTs of humans were faster in both priming conditions than in the Neutral condition, suggesting that expectation of a target facilitated search (“Y” predicted “A” and “D” predicted “E”). In contrast, the pigeons showed no evidence of expectation-based facilitation, with constant slowing effects of the Target prime extending across sessions. Possible mechanisms underlying such a slowing priming effect in pigeons were discussed.     

Cerebral perfusion pressure in giraffe: modelling the effects of head-raising and -lowering

Loss of consciousness caused by positional changes of the head results from reduced cerebral blood flow (CBF). CBF is related to cerebral perfusion pressure (CPP). CPP is the difference between mean arterial pressure (MAP) at the head and intracranial pressure (ICP). The positional change of the giraffe head between ground level and standing upright is the largest of all animals yet loss of consciousness does not occur. We have investigated the possibility that an increase in CPP protects giraffe from fainting, using a mechanical model that functioned as an anatomical U-tube. It consisted of a rigid ascending “carotid” limb, a collapsible “brain” tube drained by a rigid, “vertebral venous plexus” (VVP) tube, and a collapsible “head” tube drained by a collapsible tube representing the “jugular vein”. The descending tubes could be rotated relative to the “carotid” tube to be horizontal, or at 30°, 45°, and 60° to the vertical to simulate changes in head position. Pressure at the top of the “carotid” tube was intracranial MAP, at the top of the “VVP” tube was ICP, and the difference CPP. In the simulated “head-up” position and a fluid flow rate of 4 L min⁻¹, CPP was ∼170 mmHg. With the VVP tube horizontal, CPP fell from ∼170 to 45 mmHg, but increased to ∼67 mmHg at 30° “down”, to ∼70 mmHg at 45° “down” and to ∼75 at 60° “down”. The fall in CPP in the head-down positions resulted from a decrease in viscous resistance in, and dissipation of pressure to, the “head” and “jugular” tubes. These data provide an estimate of cranial pressure changes in giraffe during positional changes of the head, and suggest that an increase in CPP plays a significant role in maintaining CBF during head-raising and that it may be an important mechanism for preventing fainting in giraffe.     

Amino-terminal domain interactions of lambda integrase on arm-type DNA

In contrast to the other tyrosine recombinase family members, integrase protein (Int) of bacteriophage λ has an additional amino-terminal domain that binds to “arm-type” DNA sequences distant from those involved in strand exchange. The homomeric interaction between neighboring amino-terminal domains of Int is contributed by R30-D71 salt-bridge in a non-equivalent manner on Holliday-junction intermediates. In this report, R30 and D71 residues were investigated in regard to Int’s cooperative binding to “arm-type” DNA and the attenuating function of “arm-type” DNA. The results suggest the electrostatic interaction between residues 30 and 71 is dependent on “arm-type” DNA and contributes the “selective” inhibition of catalytic activity of λ Int by “arm-type” DNA.     

Quantum Zeno features of bistable perception

A generalized quantum theoretical framework, not restricted to the validity domain of standard quantum physics, is used to model the dynamics of the bistable perception of ambiguous visual stimuli such as the Necker cube. The central idea is to treat the perception process in terms of the evolution of an unstable two-state system. This gives rise to a Necker-Zeno effect, in analogy to the quantum Zeno effect. A quantitative relation between the involved time scales is theoretically derived. This relation is found to be satisfied by empirically obtained cognitive time scales relevant for bistable perception.     

Neurodegenerative disease-specific induced pluripotent stem cell research

Neurodegenerative disease-specific induced pluripotent stem cell (iPSC) research contributes to the following 3 areas; “Disease modeling”, “Disease material” and “Disease therapy”.“Disease modeling”, by recapitulating the disease phenotype in vitro, will reveal the pathomechanisms. Neurodegenerative disease-specific iPSC-derived non-neuronal cells harboring disease-causative protein(s), which play critical roles in neurodegeneration including motor neuron degeneration in amyotrophic lateral sclerosis, could be “Disease material”, the target cell(s) for drug screening. These differentiated cells also could be used for “Disease therapy”, an autologous cellular replacement/neuroprotection strategy, for patients with neurodegenerative disease.Further progress in these areas of research can be made for currently incurable neurodegenerative diseases.