How do potentials derived from structural databases relate to “true” potentials?

Knowledge-based potentials are used widely in protein folding and inverse folding algorithms. Two kinds of derivation methods are used. (1) The interactions in a database of known protein structures are assumed to obey a Boltzmann distribution. (2) The stability of the native folds relative to a manifold of misfolded structures is optimized. Here, a set of previously derived contact and secondary structure propensity potentials, taken as the "true" potentials, are employed to construct an artificial protein structural database from protein fragments. Then, new sets of potentials are derived to see how they are related to the true potentials. Using the Boltzmann distribution method, when the stability of the structures in the database lies within a certain range, both contact potentials and secondary structure propensities can be derived separately with remarkable accuracy. In general, the optimization method was found to be less accurate due to errors in the "excess energy" contribution. When the excess energy terms are kept as a constraint, the true potentials are recovered exactly.     

How Quickly do Fragments of Coral “Self‐Attach” after Transplantation?

Transplantation of coral fragments is seen as a potential method to rapidly restore coral cover to areas of degraded reef; however, considerable research is still needed to assess the effectiveness of coral transplantation as a viable reef restoration tool. Initially, during restoration efforts, coral transplants are attached artificially. Self‐attachment (i.e., growth of coral tissue onto the substrate) provides a more secure and lasting bond, thus knowledge about self‐attachment times for corals is of importance to reef restoration. While it is known that coral fragments may generate new tissue and bond to substrata within a few weeks of transplantation, surprisingly little is known about the speed of self‐attachment for most species. Two independent experiments were carried out to examine the self‐attachment times of 12 scleractinian and one non‐scleractinian coral species to a natural calcium carbonate substrate. The first experiment examined times to self‐attachment in 11 species of differing morphologies from seven families over approximately 7 months, whereas the second experiment examined three fast‐attaching Acropora species over approximately 1 month. In the first experiment, the branching species Acropora muricata had a significantly faster self‐attachment time compared to all other species, while Echinopora lamellosa had the slowest self‐attachment time. For the second experiment, A. muricata was significantly slower to self‐attach than Acropora hyacinthus (tabular) and Acropora digitifera (corymbose‐digitate). The results suggest that a combination of factors including growth rates, growth form and life history may determine how quickly fragments of coral species self‐attach after fragmentation and transplantation.     

“The” genetic code?

The DNA‐based code for protein through messenger and transfer RNA is widely regarded as the code of life. But genomes are littered with other kinds of coding elements as well, and all of them probably came after a supercode for the tRNA system itself.     

Does “supersaturated coexistence” resolve the “paradox of the plankton”?

In contradiction with field observations, theory predicts that the number of coexisting plankton species at equilibrium cannot exceed the number of limiting resources, which is called the "paradox of the plankton". Recently, Huisman & Weissing (1999 , 2000 ) showed, in a model study, that the number of coexisting species may exceed the number of limiting resources when internal system feedback induces oscillations or chaos. In this paper, we use the term "supersaturated coexistence" for this phenomenon. On the basis of these findings, they claimed that the paradox of the plankton is solved. We investigated the prerequisites for supersaturated coexistence in the same model. Our results indicate that supersaturated coexistence is a rare phenomenon in parameter space, requires a very precise parameterization of the community members and is sensitive to the introduction of new species and the removal of the present species. This raises the question of whether supersaturated coexistence is likely to occur in nature. We conclude that the claim by Huisman & Weissing (1999 , 2000 ) is premature.     

Was heißt “lebendig”?

“Life” means “being alive” of special entities, which we call “organisms”. From a physical point of view, living entities are open systems, which exchange matter as well as energy with their surroundings. Against disruptive influences permanently present, they maintain actively and autonomously a steady state far from the thermodynamic equilibrium. This dynamic state of living beings represents a functional order, an internal “organization”. That means that the involved processes one and all must be correlated in such a way that they in sum prevent the breakdown of the living state. Organization implies functionality, which in turn requires structural relationships, and structures require information for their specification. Information in turn presupposes a source, which is constituted in living systems by the nucleic acids. Organisms are unique in having a capacity to use information, which is stored in the nucleic acid and yields the basis for their specific internal organization in its perpetuation: Living beings, and only they, show a self‐maintained organization.     

Parrot claylick distribution in South America: do patterns of “where” help answer the question “why”?

Geophagy is well known among some Neotropical parrots. The clay apparently adsorbs dietary toxins and/or provides supplemental nutrients. We used location data and 23 environmental layers to develop a predictive model of claylick distribution using Maxent software. We related species characteristics to claylick use and examined how parrot assemblages using claylicks changed with distance from the centre of claylick distribution. Fifty‐two parrot claylicks were reported from an area of ca 4 million km² but over 50% were restricted to a 35 000 km² region of southeast Peru and northern Bolivia. Claylicks were strongly associated with moist forest on younger (<65 millions of yr) geological formations and exposed river banks. The predictive model of claylick distribution matched our reported range well, with precipitation of warmest quarter, land cover, temperature seasonality, and distance from the ocean being most important predictors of claylick presence. Twenty‐six of the region's 46 parrot species visited claylicks. Species differed greatly in their lick use, but body size, dietary breadth, abundance and other traits were poor predictors of lick use. We are confident that our survey identified the distribution of major parrot claylicks in South America, although less conspicuous parrot geophagy may occur elsewhere. We suggest that claylick distribution reflects both underlying geology (allowing claylick formation in only some regions) and the physiological need for geophagy among parrots in different parts of the continent. Data on the latter are inconclusive, but we argue that parrot claylick distribution supports the contention that geophagy is related more to sodium deficiencies than to protection from dietary toxins.     

Revisiting “what do tadpoles really eat?” A 10‐year perspective

1. Tadpoles are diverse and abundant consumers, and knowledge of their feeding ecology and trophic status is essential in understanding their functional roles within aquatic habitats. Here we revisit Altig, Whiles, and Taylor (2007)'s paper, which highlighted the knowledge gaps in tadpole feeding ecology and the application of modern techniques, such as stable isotope and fatty acid analyses to better quantify dominant food resources, food assimilation, and the trophic status of tadpoles.
2. We reviewed the ecological studies that have been published since 2007 that used stable isotopes and fatty acid analyses, also metagenomics and ecological stoichiometry analyses. We describe the ecological roles of tadpoles in freshwater ecosystems and identify knowledge gaps regarding tadpole feeding ecology across biogeographic regions.
3. Worldwide declines in amphibian abundance and diversity create an urgent need to document their feeding ecology and trophic status. As consumers, tadpoles play important functional roles in nutrient cycling, energy flow, and bioturbation. They also exhibit context‐dependent trophic plasticity in response to abiotic and biotic gradients, which complicates understanding of their trophic roles.
4. Most studies of tadpole trophic ecology have been conducted primarily on species from the families Ranidae, Bufonidae, and Hylidae from Neotropic and Nearctic regions, while species in tropical regions such as Africa and Asia lack ecological information for tadpoles. There continues to be a need for studies of tadpole diets and/or trophic ecology in Africa and Southeast Asia regions where species endemism is threated by the growth of anthropogenic activities.
5. The majority of studies have focused on trophic ecology of tadpoles from the perspective of single species or at relatively small spatial and temporal scales. Studies that address questions from an ecosystem perspective were scarce, but are critical for conservation and management. Future research should aim to address the role of tadpoles as consumers across broader spatiotemporal scales.

     

Tropicality and abjection: What do we really mean by “Neglected Tropical Diseases”?

Neglected tropical diseases are defined operationally as diseases that prevail in “tropical” regions and are under‐researched, under‐funded, and under‐treated compared with their disease burden. By analysing the adjectives “tropical” and “neglected,” I expose and interrogate the discourses within which the term “neglected tropical disease” derives its meaning. First, I argue that the term “tropical” conjures the notion of “tropicality,” a form of Othering which erroneously explains the disease‐prevalence of “tropical” regions by reference to environmental determinism, rather than colonialism and neocolonialism. Second, I examine the way in which this Othering enables the abjection of tropical regions and their peoples, leading to neglect. I recommend that the term “neglected tropical diseases” be more carefully contextualised within health scholarship, education, and policy.     

What are genes “for” or where are traits “from”? What is the question?

For at least a century it has been known that multiple factors play a role in the development of complex traits, and yet the notion that there are genes “for” such traits, which traces back to Mendel, is still widespread. In this paper, we illustrate how the Mendelian model has tacitly encouraged the idea that we can explain complexity by reducing it to enumerable genes. By this approach many genes associated with simple as well as complex traits have been identified. But the genetic architecture of biological traits, or how they are made, remains largely unknown. In essence, this reflects the tension between reductionism as the current “modus operandi” of science, and the emerging knowledge of the nature of complex traits. Recent interest in systems biology as a unifying approach indicates a reawakened acceptance of the complexity of complex traits, though the temptation is to replace “gene for” thinking by comparably reductionistic “network for” concepts. Both approaches implicitly mix concepts of variants and invariants in genetics. Even the basic question is unclear: what does one need to know to “understand” the genetic basis of complex traits? New operational ideas about how to deal with biological complexity are needed.     

Is cyclin Zeuthen's “division protein”?

Biochemical evidence is presented for the presence of cyclin in Tetrahymena. Zeuthen previously postulated the existence of a heat-labile “division protein” to explain heat-shock-induced division synchrony in Tetrahymena [(1964) Synchrony in Cell Division and Growth (Zeuthen, E., Ed.), pp. 99–158, Interscience, New York]. We show that cyclin is heat-labile in Tetrahymena and suggest that cyclin may be Zeuthen's division protein. Cyclin and cell cycle control is of interest in Tetrahymena because the division mechanism drives macronuclear amitosis, closed and acentric micronuclear mitosis, and cortical differentiation in this cell type.     

Do “heavy” eaters live longer?

A new hypothesis is put forward, linking cellular endurance with dietary consumption of stable heavy isotopes. Due to the isotope effect, biomolecules that incorporate heavier isotopes give rise to more stable molecular structures with increased resistance to damages associated with aging and age-related disease. The inclusion of heavy isotopes might be either active (selection for heavier isotopes) or passive (incorporation reflecting the existing abundance). The hypothesis links consumption of foods relatively rich in heavy isotopes (such as (13)C and D, derived from C4-plants), especially at the early stages of the organism's development, with enhanced longevity. Implications of diets and intestinal microflora are also discussed.     

Mitochondrial biogenesis: Which part of “NO” do we understand?

A recent paper by Nisoli et al. [1] provides the first evidence that elevated levels of nitric oxide (NO) stimulate mitochondrial biogenesis in a number of cell lines via a soluble guanylate-cyclase-dependent signaling pathway that activates PGC1alpha (peroxisome proliferator-activated receptor gamma coactivator-1alpha), a master regulator of mitochondrial content. These results raise intriguing possibilities for a role of NO in modulating mitochondrial content in response to physiological stimuli such as exercise or cold exposure. However, whether this signaling cascade represents a widespread mechanism by which mammalian tissues regulate mitochondrial content, and how it might integrate with other pathways that control PGC1alpha expression, remain unclear.     

PAIRED PREFERENCE “PLACEBO” TESTS WITH “IDENTICAL” STIMULI: DOES INTRODUCING GRADED PREFERENCE RESPONSES AFFECT THE FREQUENCY OF “NO PREFERENCE” RESPONSES?

In the placebo control condition for paired preference testing, identical stimuli are presented to consumers to determine the frequency of preference and no preference responses induced by the hidden demand characteristics of the testing condition. As a control for bias, induced by such hidden demand characteristics, these frequencies can be compared with the actual preference frequencies of the nonidentical test stimuli to be assessed for preference. It was hypothesized that the introduction of graded preference response options might reduce the frequency of no preference responses in the placebo condition. Using identical yogurt stimuli with related-sample (single-group) and independent-sample (multigroup) designs, this hypothesis was not confirmed.

PRACTICAL APPLICATIONS

The placebo condition in paired preference testing provides a way to control the tendency of consumers to give false preference. The statistical analysis can be improved by finding a protocol that maximizes the proportion of no preference responses in the placebo condition. This can be done by increasing the number of response options that imply no preference. Yet, there is sometimes a desire to increase the number of preference options by using graded responses for preference strength. Does this alter the dynamics of the ever-important placebo condition by reducing the number of no preference responses? This project found that any effect was minimal.     

Why do nocturnal grasshoppers and katydids “salute” to flash photography?

Nocturnal animals can be sensitive to powerful light from the environment. Anthropogenically induced perturbation to natural light regimes, including ecological light pollution and flash photography, can have wide‐reaching implications on the ecology and behavior. Ecological ramifications of strong lights were traditionally focused on vertebrates although there is now more focus on invertebrates. Nonetheless, there are still unanswered questions on visual ecology and evolution, particularly on individual‐level effects and of tropical species. Specifically, how invertebrate individuals react to strong light is generally undocumented. Based on opportunistic surveys around Southeast Asia, orthopterans, spotted using concentrated torchlight and exposed to sudden strong light intensity during flash macrophotography, were observed to screen themselves by positioning their foreleg over the dorsum of the compound eye. This resembled the orthopteran “saluting” to the camera. These observations provided empirical evidence of how high intensity light can unsettle orthopterans and other insects and further ecological and evolutionary hypotheses and questions can be raised to understand the effect of light pollution.     

“How pendulum‐like are siamangs? energy exchange during brachiation”

Hylobatidae (gibbons and siamangs) are known for their brachiation skills. The comparison of brachiation with a pendulum is made several times in the literature, and the costs and benefits of being pendulum-like are well described. However, the amount of energy exchange during brachiation of gibbons has rarely been determined. In this study, the amount of energy recovery (ER) during brachiation is assessed for three siamangs in a seminatural environment. The animals were recorded by four cameras while voluntarily brachiating on three different setups. The effects of locomotion speed, brachiation type, and setup on ER as well as on the external mechanical work during brachiation are determined. It is hypothesized that the amount of ER decreases with an increasing setup complexity while the external mechanical work increases. Additionally, we expect that support arm kinematics will be adjusted according to spatial complexity in order to maintain high recovery percentages. Our results show that ER is mainly determined by brachiation speed. Regardless of type of brachiation or setup, brachiation is done with a lower ER when brachiating faster. Within our limited range of setup variation, the expected effect of increasing complexity is not found. Although there is significant variation in support arm joint angles, no clear relation with speed, brachiation type, or setup is observed.