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.     

Does the “C3 effect” offset the Δ2 effect,as regards the solution flexibility of aldoses?

The solution flexibility of carbohydrates influences a variety of molecular recognition and regulatory processes. For aldoses and other monosaccharides, this flexibility is dictated by the orientations of the various hydroxyl (OH) groups present, which influences conformer and anomer ratios, interactions among these OH groups, and interactions between them and the surrounding solvent. Depending on the number and position of axial OH groups, a variety of structures can coexist in solutions at equilibrium. In 1950, as part of his pioneering studies on the shape of pyranoside rings, Reeves described the Δ2 effect, the greater destabilization of the pyranose ring conformation when the OH group on carbon 2 (C₂) is in the axial position. It was later proposed by Angyal that the Δ2 effect could be cancelled by the presence of an axial OH on C₃, termed here the “C₃ effect.” Employing size‐exclusion chromatography, an entropically‐controlled separation technique, we have investigated whether or not the C₃ and Δ2 effects indeed do compensate for one another with respect to their influence on the solution flexibility of select aldohexoses and aldopentoses. As will be seen, while qualitatively and semiquantitatively this mutual cancellation of effects does occur in aldohexoses, it does not appear to do so in aldopentoses. An explanation for the latter appears to lie in the variety of anomers and conformers present in equilibrium solutions of those aldopentoses studied and in the relative entropic contribution of individual conformers or anomers to the total solution flexibility. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 703–711, 2014.     

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.     

Is the concept of “control group” valid? A quantitative comparison of behavior of caged baboon groups

Behavioral comparisons between six caged baboon groups indicate that the groups have consistent and similar behavioral attributes. At the same time it is possible to distinguish between classes of animals in each group such as males versus females and high status versus low status rank. Comparable results are obtained in both ANOVA and Kruskal-Wallis one-way analysis of variance by ranks. This investigation supports the assumption that baboon groups exhibit behaviors that are both consistent and predictable where environment and group composition are controlled. Thus there appears to be a strong species-appropriate set of behaviors. Behavioral plasticity and group variability might be due largely to a combination of environmental stimuli and the particular history of that group. Differential individual histories or idiosyncracies do not invalidate experimental designs which rely on randomization to structure control groups.     

Are the Kow Swamp hominids “archaic”?

Initial reports of hominids recovered at Kow Swamp, in the Murray Valley of Victoria indicated that, on the basis of cranial analyses, there was a "survival of Homo erectus features in Australia until as recently as 10,000 years ago (Thorne and Macumber, 1972, p. 316). This claim was later refuted by others, who suggested that artificial cranial deformation may have been responsible for at least some of the distinctive and "primitive" traits seen in the Kow Swamp individuals. Previous research by this worker and others has indicated that taxonomic traits at both specific and subspecific levels are present in hominine femora. Therefore, it may be possible to evaluate the "primitiveness" of the Kow Swamp sample on the basis of their femoral anatomy. Morphometric analyses were undertaken, using as controls femora of Romano British, Tasmanian, and other Murray Valley populations. On the basis of bivariate and multivariate analyses it was found that, at least in this single element of the postcranium, no primitive features were present. The Kow Swamp sample, in fact, shows a very close morphometric relationship with all included Homo sapiens controls and is significantly distinct from Homo erectus.     

Survivin study: An update of “What is the next wave?”

Studies on survivin over the past 2-3 years have shown that survivin possesses multiple subcellular localizations and is a multifunctional molecule involved in many aspects of cellular processes and/or behaviors. The subcellular localization and function of the survivin splice variants, however, have not yet been well elucidated. We have, therefore, provided additional observations on several survivin splice variants for further exploration. This review article will update the role of survivin, and its splice variants in the mitosis/cell cycle, apoptosis, tumorigenesis, chemoprevention, drug/radiation resistance, and cancer therapeutics.     

What are the dielectric “constants” of proteins and how to validate electrostatic models?

Implicit models for evaluation of electrostatic energies in proteins include dielectric constants that represent effect of the protein environment. Unfortunately, the results obtained by such models are very sensitive to the value used for the dielectric constant. Furthermore, the factors that determine the optimal value of these constants are far from being obvious. This review considers the meaning of the protein dielectric constants and the ways to determine their optimal values. It is pointed out that typical benchmarks for validation of electrostatic models cannot discriminate between consistent and inconsistent models. In particular, the observed pK(a) values of surface groups can be reproduced correctly by models with entirely incorrect physical features. Thus, we introduce a discriminative benchmark that only includes residues whose pK(a) values are shifted significantly from their values in water. We also use the semimacroscopic version of the protein dipole Langevin dipole (PDLD/S) formulation to generate a series of models that move gradually from microscopic to fully macroscopic models. These include the linear response version of the PDLD/S models, Poisson Boltzmann (PB)-type models, and Tanford Kirkwwod (TK)-type models. Using our different models and the discriminative benchmark, we show that the protein dielectric constant, epsilon(p), is not a universal constant but simply a parameter that depends on the model used. It is also shown in agreement with our previous works that epsilon(p) represents the factors that are not considered explicitly. The use of a discriminative benchmark appears to help not only in identifying nonphysical models but also in analyzing effects that are not reproduced in an accurate way by consistent models. These include the effect of water penetration and the effect of the protein reorganization. Finally, we show that the optimal dielectric constant for self-energies is not the optimal constant for charge-charge interactions.     

How “representative” is the Terry collection? Evidence from the proximal femur

The work reported here is the beginning of an attempt to determine whether data on skeletal aging changes derived from the Terry collection (Smithsonian Institution) can safely be applied to present-day clinical and forensic problems. Measurements made on radiographs of the proximal third of the right femur below the greater trochanter were compared in three groups of American white females: Terry collection “regulars,” Terry collection willed, and GW (George Washington University Medical Center) willed. Mean birth year for the Terry regulars was 1883, whereas the mean birth year for Terry and GW willed was 1910. Terry willed femora are longer than those of Terry regulars, but not more robust. The two groups show opposing secular trends in femoral length, and in this respect the Terry regulars appear closer to the general U.S. population. In two indices of relative medullary cavity size (which reflect changes in cortical thickness as well as internal and external diameters) all three groups agree in showing age-related increase of medullary diameters, greater increase in the anterior–posterior dimension, and greatest amount of increase at diaphyseal levels. The major difference between groups is in timing, with medullary cavity expansion becoming evident at least a decade earlier and leading to greater eventual loss of cortical thickness in the willed groups.     

Is REP a measure of “objective support”?

Grant and Kluge have recently stated that Bremer support and their own REP (“relative explanatory power”), are the only objective measures of group support. This paper discusses their claim, showing that their philosophical arguments have no basis, and that their own numerical examples actually serve to illustrate shortcomings of REP.     

A historical biogeography of megadiverse Sericini—another story “out of Africa”?

Megadiverse insect groups present special difficulties for biogeographers because poor classification, incomplete knowledge of taxonomy, and many undescribed species can introduce a priori sampling bias to any analysis. The historical biogeography of Sericini, a tribe of melolonthine scarabs comprising about 4000 species, was investigated using the most comprehensive and time‐calibrated molecular phylogeny available today. Problems arising through nomenclatural confusion were overcome by extensive sampling (665 species) from all major lineages of the tribe. A West Gondwanan origin of Sericini (c. 112 Ma) was reconstructed using maximum parsimony, maximum‐likelihood and model‐based ancestral area estimation. Vicariance in the tribe's earliest history separated Neotropical and Old World Sericini, whereas subsequent lower Cretaceous biogeography of the tribe was characterized by repeated migrations out of Africa, resulting in the colonization of Eurasia and Madagascar. North America was colonized from Asia during the Cenozoic and a lineage of “Modern Sericini” reinvaded Africa. Diversification dynamics revealed three independent shifts to increased speciation rates: in African ant‐adapted Trochalus, Oriental Tetraserica, and Asian and African Sericina. Southern Africa is proposed as both cradle and refuge of Sericini. This area has retained many old lineages that portray the evolution of the African Sericini fauna as a series of taxon pulses.     

Who's afraid of the big bad Wolff?: “Wolff's law” and bone functional adaptation

"Wolff's law" is a concept that has sometimes been misrepresented, and frequently misunderstood, in the anthropological literature. Although it was originally formulated in a strict mathematical sense that has since been discredited, the more general concept of "bone functional adaptation" to mechanical loading (a designation that should probably replace "Wolff's law") is supported by much experimental and observational data. Objections raised to earlier studies of bone functional adaptation have largely been addressed by more recent and better-controlled studies. While the bone morphological response to mechanical strains is reduced in adults relative to juveniles, claims that adult morphology reflects only juvenile loadings are greatly exaggerated. Similarly, while there are important genetic influences on bone development and on the nature of bone's response to mechanical loading, variations in loadings themselves are equally if not more important in determining variations in morphology, especially in comparisons between closely related individuals or species. The correspondence between bone strain patterns and bone structure is variable, depending on skeletal location and the general mechanical environment (e.g., distal vs. proximal limb elements, cursorial vs. noncursorial animals), so that mechanical/behavioral inferences based on structure alone should be limited to corresponding skeletal regions and animals with similar basic mechanical designs. Within such comparisons, traditional geometric parameters (such as second moments of area and section moduli) still give the best available estimates of in vivo mechanical competence. Thus, when employed with appropriate caution, these features may be used to reconstruct mechanical loadings and behavioral differences within and between past populations.     

“How Local Is Local?”—A Review of Practical and Conceptual Issues in the Genetics of Restoration

In plant conservation, restoration (the augmentation or reestablishment of an extinct population or community) is a valuable tool to mitigate the loss of habitat. However, restoration efforts can result in the introduction of novel genes and genotypes into populations when plant materials used are not of local origin. This movement is potentially important because many plant species are subdivided into populations that are adapted to local environmental conditions. Here we focus on genetic concerns arising from ongoing restoration efforts, where often little is known about “How local is local?” (i.e., the geographic or environmental scale over which plant species are adapted). We review the major issues regarding gene flow and local adaptation in the restoration of natural plant populations. Finally, we offer some practical, commonsense guidelines for the consideration of genetic structure when restoring natural plant populations.     

What about cultural ecosystems? Opportunities for cultural considerations in the “International Standards for the Practice of Ecological Restoration”

The Society for Ecological Restoration's 2016 (SER) “International Standards for the Practice of Ecological Restoration” is a living document intended to guide restoration projects “anywhere in the world.” Given its intended global scope and in hopes of informing future editions, this document is critically assessed in light of the role people have played in ecosystems around the world. We argue that the Standards has an underlying nature–culture dichotomization that limits its applicability; in qualifying what it calls “cultural ecosystems” for rehabilitation, rather than restoration, the Standards privileges colonial visions of ecological restoration. We also discuss the Standards' representation of the ecological impacts and practices of indigenous groups. Whereas the Standards claims that preindustrial cultural ecosystems exist in states similar to unmodified areas, many historians, anthropologists, and paleoecologists would point out that preindustrial people sometimes had massive environmental impacts through agriculture, hydrological engineering, over‐hunting, living in dense urban environments, transporting species, burning on a scale capable of changing the climate, and other practices. Furthermore, the Standards does not discuss how the cultural goals of indigenous groups fit into the overall picture of ecological restoration. Future drafts of the Standards should more accurately frame the diverse roles people play in nature, and create global standards that account for the validity of cultural goals for ecological restoration.     

What is the role of the second “structural” NADP+‐binding site in human glucose 6‐phosphate dehydrogenase?

Human glucose 6-phosphate dehydrogenase, purified after overexpression in E. coli, was shown to contain one molecule/subunit of acid-extractable "structural" NADP+ and no NADPH. This tightly bound NADP+ was reduced by G6P, presumably following migration to the catalytic site. Gel-filtration yielded apoenzyme, devoid of bound NADP+ but, surprisingly, still fully active. Mr of the main component of "stripped" enzyme by gel filtration was approximately 100,000, suggesting a dimeric apoenzyme (subunit Mr = 59,000). Holoenzyme also contained tetramer molecules and, at high protein concentration, a dynamic equilibrium gave an apparent intermediate Mr of 150 kDa. Fluorescence titration of the stripped enzyme gave the K d for structural NADP+ as 37 nM, 200-fold lower than for "catalytic" NADP+. Structural NADP+ quenches 91% of protein fluorescence. At 37 degrees C, stripped enzyme, much less stable than holoenzyme, inactivated irreversibly within 2 d. Inactivation at 4 degrees C was partially reversed at room temperature, especially with added NADP+. Apoenzyme was immediately active, without any visible lag, in rapid-reaction studies. Human G6PD thus forms active dimer without structural NADP+. Apparently, the true role of the second, tightly bound NADP+ is to secure long-term stability. This fits the clinical pattern, G6PD deficiency affecting the long-lived non-nucleate erythrocyte. The Kd values for two class I mutants, G488S and G488V, were 273 nM and 480 nM, respectively (seven- and 13-fold elevated), matching the structural prediction of weakened structural NADP+ binding, which would explain decreased stability and consequent disease. Preparation of native apoenzyme and measurement of Kd constant for structural NADP+ will now allow quantitative assessment of this defect in clinical G6PD mutations.