How Reliable are Density Estimates for Diurnal Primates?

Primate population assessments provide the basis for comparative studies and are necessary prerequisites in determining conservation status. The most widely used assessment method is line transect sampling, which generates systematic data quickly and comparatively inexpensively. In contrast, the presumably most reliable method is long-term monitoring of known groups, which is both slow and costly. To assess the reliability of various analytical methods, we compared group and population densities for white-handed gibbons (Hylobates lar carpenteri) and Phayre’s leaf monkeys (Trachypithecus phayrei crepusculus) derived from transect walks with those from long-term group follows at Phu Khieo Wildlife Sanctuary, Thailand. Our assistants and we regularly walked a 4-km transect over 30 mo (480 km total), resulting in 155 gibbon sightings and 125 leaf monkey sightings. We then estimated densities via 1) DISTANCE and 2) the Kelker method based on perpendicular distances (PD) or animal-to-observer distances (AOD). We compared the 3 estimates to values based on known home ranges (95% kernels), accounting for home range overlap, combined with group size data. Analyses of line transect data consistently overestimated group densities for both species, while underestimating group size for leaf monkeys. Quality of results varied according to the group size and spread of each species. However, we found, in accordance with previous studies, that values derived via AOD (or its derivations) matched most closely with population estimates based on home range data.     

How Reliable are the Methods for Estimating Repertoire Size?

Quantifying signal repertoire size is a critical first step towards understanding the evolution of signal complexity. However, counting signal types can be so complicated and time consuming when repertoire size is large, that this trait is often estimated rather than measured directly. We studied how three common methods for repertoire size quantification (i.e., simple enumeration, curve‐fitting and capture‐recapture analysis) are affected by sample size and presentation style using simulated repertoires of known sizes. As expected, estimation error decreased with increasing sample size and varied among presentation styles. More surprisingly, for all but one of the presentation styles studied, curve‐fitting and capture–recapture analysis yielded errors of similar or greater magnitude than the errors researchers would make by simply assuming that the number of types in an incomplete sample is the true repertoire size. Our results also indicate that studies based on incomplete samples are likely to yield incorrect ranking of individuals and spurious correlations with other parameters regardless of the technique of choice. Finally, we argue that biological receivers face similar difficulties in quantifying repertoire size than human observers and we explore some of the biological implications of this hypothesis.     

How are proliferation and differentiation of melanocytes regulated?

Coat colors are determined by melanin (eumelanin and pheomelanin). Melanin is synthesized in melanocytes and accumulates in special organelles, melanosomes, which upon maturation are transferred to keratinocytes. Melanocytes differentiate from undifferentiated precursors, called melanoblasts, which are derived from neural crest cells. Melanoblast/melanocyte proliferation and differentiation are regulated by the tissue environment, especially by keratinocytes, which synthesize endothelins, steel factor, hepatocyte growth factor, leukemia inhibitory factor and granulocyte-macrophage colony-stimulating factor. Melanocyte differentiation is also stimulated by alpha-melanocyte stimulating hormone; in the mouse, however, this hormone is likely carried through the bloodstream and not produced locally in the skin. Melanoblast migration, proliferation and differentiation are also regulated by many coat color genes otherwise known for their ability to regulate melanosome formation and maturation, pigment type switching and melanosome distribution and transfer. Thus, melanocyte proliferation and differentiation are not only regulated by genes encoding typical growth factors and their receptors but also by genes classically known for their role in pigment formation.     

Fluctuation Tests: How Reliable Are the Estimates of Mutation Rates?

Fifty one years ago, Luria and Delbruck published in Genetics a paper that was to become a classic. In it they proved, beyond all reasonable doubt, that bacteria were mutating to phage resistance long before they could have encountered any bacteriophage. Luria and Delbruck also showed how the same experimental data could be used to estimate bacterial mutation rates. Since that time and in many different contexts the methods that they introduced have been used to estimate mutation rates. However, little seems to be known about the errors to be expected in such estimates. In what follows I examine how much uncertainty in the estimates is to be expected merely on the basis of the stochastic variability inherent in the sampling process. On the basis of this examination I question a few traditional ideas and conclude with some practical suggestions. The results were obtained by simulation. It is my hope that they may inspire others to provide a rigorous theoretical basis for such calculations.     

Cancer and diet: How are they related?

Extensive research in the past decade has revealed cancer to be a multigenic disease caused by perturbation of multiple cell signalling pathways and dysregulation of numerous gene products, all of which have been linked to inflammation. It is also becoming evident that various lifestyle factors, such as tobacco and alcohol use, diet, environmental pollution, radiation and infections, can cause chronic inflammation and lead to tumourigenesis. Chronic diseases caused by ongoing inflammation therefore require chronic, not acute, treatment. Nutraceuticals, compounds derived from fruits, vegetables, spices and cereals, can be used chronically. This study discusses the molecular targets of some nutraceuticals that happen to be markers of chronic inflammation and how they can prevent or treat cancer. These naturally-occurring agents in the diet have great potential as anti-cancer drugs, thus proving Hippocrates, who proclaimed 25 centuries ago, 'Let food be thy medicine and medicine be thy food'.     

Prediction of peptide structure: How far are we?

Rational design of peptides is a challenge, which would benefit from a better knowledge of the rules of sequence-structure-function relationships. Peptide structures can be approached by spectroscopy and NMR techniques but data from these approaches too frequently diverge. Structures can also be calculated in silico from primary sequence information using three algorithms: Pepstr, Robetta, and PepLook. The most recent algorithm, PepLook introduces indexes for evaluating structural polymorphism and stability. For peptides with converging experimental data, calculated structures from PepLook and, to a lesser extent from Pepstr, are close to NMR models. The PepLook index for polymorphism is low and the index for stability points out possible binding sites. For peptides with divergent experimental data, calculated and NMR structures can be similar or, can be different. These differences are apparently due to polymorphism and to different conditions of structure assays and calculations. The PepLook index for polymorphism maps the fragments encoding disorder. This should provide new means for the rational design of peptides.     

How optimal are the binding energetics of barnase and barstar?

The extracellular ribonuclease barnase and its intracellular inhibitor barstar bind fast and with high affinity. Although extensive experimental and theoretical studies have been carried out on this system, it is unclear what the relative importance of different contributions to the high affinity is and whether binding can be improved through point mutations. In this work, we first applied Poisson-Boltzmann electrostatic calculations to 65 barnase-barstar complexes with mutations in both barnase and barstar. The continuum electrostatic calculations with a van der Waals surface dielectric boundary definition result in the electrostatic interaction free energy providing the dominant contribution favoring barnase-barstar binding. The results show that the computed electrostatic binding free energy can be improved through mutations at W44/barstar and E73/barnase. Furthermore, the determinants of binding affinity were quantified by applying COMparative BINding Energy (COMBINE) analysis to derive quantitative structure-activity relationships (QSARs) for the 65 complexes. The COMBINE QSAR model highlights approximately 20 interfacial residue pairs as responsible for most of the differences in binding affinity between the mutant complexes, mainly due to electrostatic interactions. Based on the COMBINE model, together with Brownian dynamics simulations to compute diffusional association rate constants, several mutants were designed to have higher binding affinities than the wild-type proteins.     

Pulse domestication and cereal domestication: How different are they?

Evidence is brought to indicate that the domestication of lentil and pea is not very different from that of wheat and barley. All these Near East crops are characterized by basically the same domestication traits the key elements of which are breakdown of the wild mode of seed dispersal and loss of germination regulation. It is argued that both in the pulses and in the cereals these traits evolved in the same way. The changes are best explained by assuming that mutations causing the loss of the wild-type adaptations were automatically selected for soon after people transferred the wild progenitors into a system of planting and reaping.     

Patterns of resource partitioning by nesting herons and ibis: How are odonata exploited?

Herons and ibis are colonially nesting waders which, owing to their number, mobility and trophic role as top predators, play a key role in aquatic ecosystems. They are also good biological models to investigate interspecific competition between sympatric species and predation; two processes which structure ecological communities. Odonata are also numerous, diverse, mobile and can play an important role in aquatic ecosystems by serving as prey for herons and ibis. A relationship between prey size and bird predator has been observed in Numidia wetlands (NE Algeria) after analyzing food boluses regurgitated by six species of birds (Purple Heron, Black-crowned Night Heron, Glossy Ibis, Little Egret, Squacco Heron and Cattle Egret) during the breeding period, which also shows a temporal gradient for the six species. Both the Levins index and preliminary multivariate analysis of the Odonata as prey fed to nestling herons and ibis, indicated a high degree of resource overlap. However, a distinction of prey based on taxonomy (suborder and family) and developmental stage (larvae or adults) reveals a clear size dichotomy with large-sized predators (Purple Heron, Black-crowned Night Heron and Glossy Ibis) preying on large preys like Aeshnids and Libellulids and small-sized predators feeding mainly on small prey like Zygoptera. Overall, the resource utilization suggests a pattern of resource segregation by coexisting nesting herons and ibis based on the timing of reproduction, prey types, prey size and foraging microhabitats.     

How are cohesin rings opened and closed?

The cohesin complex is proposed to embrace sister chromatids within its ring-like structure, in which two ATP-binding 'head' domains of an SMC (structural maintenance of chromosomes) heterodimer are linked by a kleisin subunit. Recent studies shed new light on the crucial functions of the 'hinge' domain of the SMC dimer, which is located approximately 50 nm from the head domains. An emerging idea is that the hinge and head domains cooperatively modulate cohesin-DNA interactions by opening and closing the ring in a highly regulated manner.     

How scalable and suitable are single-use bioreactors?

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How Accurate are Paleoecological Reconstructions of Early Paleontological and Archaeological Sites?

Paleoecology allows construction of paleoenvironmental models, faunal changes and evolutionary trends of paleontological taxa using modern analogs. However, when linking modern analogs to paleontological taxa in paleoecological reconstruction, differential taxonomic preservation in the fossil record has to be taken into account. Paleontologists have known the biased nature of the fossil record since Efremov’s publication on taphonomy in 1940, yet many ecological models of habitats associated with hominins in paleontological and archaeological sites in Africa and elsewhere barely address the complexity of the fossil record. We use randomly sampled ungulates from modern biomes in a comparative taxonomic abundance to demonstrate how the combination of modern thanatocoenoses and taphocoenoses, when used in reference to habitat-specific biocoenosis, produce better inferences of past habitats in paleontological and archaeological sites than approaches currently used.     

How many species of Cladocera are there?

An estimation of the number of taxa within families, genera and local faunas of Cladocera reveals that only c. 129 species (17% of all known species) may be considered as sufficiently well described (valid species), and c. 146 as rather well described (fair species) but needing further study using modern methods of investigation. The status of all other species is vague. The families Chydoridae, Daphniidae and Sididae and genera Diaphanosoma, Daphnia, (including Daphniopsis), Megafenestra, Scapholeberis, Eurycercus, Chydorus, Ephemeroporus and Pleuroxus have been comparatively studied best. The largest number of valid species is known from Europe, North America, Australia and South America, and the smallest number from Africa. Presence of large number of vague species of Cladocera negatively affects faunistic, zoogeographic, and ecological studies of continental waters.Dedicated to the memory of Professor D. J. Frey     

How meaningful are heritability estimates of liability?

It is commonly acknowledged that estimates of heritability from classical twin studies have many potential shortcomings. Despite this, in the post-GWAS era, these heritability estimates have come to be a continual source of interest and controversy. While the heritability estimates of a quantitative trait are subject to a number of biases, in this article we will argue that the standard statistical approach to estimating the heritability of a binary trait relies on some additional untestable assumptions which, if violated, can lead to badly biased estimates. The ACE liability threshold model assumes at its heart that each individual has an underlying liability or propensity to acquire the binary trait (e.g., disease), and that this unobservable liability is multivariate normally distributed. We investigated a number of different scenarios violating this assumption such as the existence of a single causal diallelic gene and the existence of a dichotomous exposure. For each scenario, we found that substantial asymptotic biases can occur, which no increase in sample size can remove. Asymptotic biases as much as four times larger than the true value were observed, and numerous cases also showed large negative biases. Additionally, regions of low bias occurred for specific parameter combinations. Using simulations, we also investigated the situation where all of the assumptions of the ACE liability model are met. We found that commonly used sample sizes can lead to biased heritability estimates. Thus, even if we are willing to accept the meaningfulness of the liability construct, heritability estimates under the ACE liability threshold model may not accurately reflect the heritability of this construct. The points made in this paper should be kept in mind when considering the meaningfulness of a reported heritability estimate for any specific disease.     

Brazilian Cerrado Folivore and Florivore Caterpillars: How Different are They?

Because of the large differences between flower buds and leaves as food resources we predict that florivore caterpillars compared with folivores would present: (1) higher degree of dietary specificity; (2) higher abundance; and (3) lower species richness. Based on emerged adults from caterpillars collected on leaves and inflorescences our results showed that the florivore fauna was strongly dominated by a few species with higher abundance and dietary specificity than the folivore fauna.