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 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.     

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.     

How scalable and suitable are single-use bioreactors?

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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 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 similar are daily and seasonal biological clocks?

Daily and seasonal timing systems in insects have usually been supposed to share similar mechanisms, because both rely in large measure on information from the daily light-dark cycle: daily clocks can ensure that activity coincides with the appropriate time of day, and seasonal time is indicated most reliably by daylength. However, several lines of evidence suggest that the systems are different. For example, receptor features, photosensitive pigments, clocks, and the effectors that mediate responses to information derived from the clock may have different daily, seasonal and general functions and properties, and several different systems are known. There are many different additional elements in the seasonal response. Therefore, these responses may not rely on similar timing mechanisms, despite the long-standing belief that the seasonal clock has circadian components. Such a difference would be consistent with the fact that temporal responses serve a very wide range of purposes, meeting many different ecological needs on different time frames. Consequently, understanding the seasonal relevance of the photoperiodic responses is more important than revealing any possible involvement with circadian systems.     

Biodiversity of living benthic foraminifera: How many species are there?

In ecological studies involving the analysis of  2.4 million living (stained) individual tests, to date  2140 species of benthic foraminifera have been recorded. Of these 602 species are agglutinated, 341 porcelaneous and 1197 hyaline. The numbers of species in the major environments are: marginal marine 701 (in  1.5 million individuals), shelf 989 (in  0.6 million individuals) and deep sea 831 (in  0.3 million individuals). 381 species occur in more than one major environment. Overall  33% have abundance of > 10% while  67% are of minor abundance (< 10%). The majority of species are rare, most are endemic and very few are cosmopolitan (5% or less). To estimate the potential total number of living species the following factors need to be quantified: the proportion of species already named (here considered unlikely to be less than 50% of the potential total), the number of species currently known to be dead but for which living representatives may yet to be found (assumed to be 5% = 107 species), and the proportion of species that are synonyms (10–25% = 214 to 535 species). Assuming that 50% of species have already been named (2140 + 107 = 2247), the potential total ranges from  3959 to  4280 species for 10% synonymy to  3210 to  3531 species for 25% synonymy.     

How cooperative are protein folding and unfolding transitions?

A thermodynamically and kinetically simple picture of protein folding envisages only two states, native (N) and unfolded (U), separated by a single activation free energy barrier, and interconverting by cooperative two‐state transitions. The folding/unfolding transitions of many proteins occur, however, in multiple discrete steps associated with the formation of intermediates, which is indicative of reduced cooperativity. Furthermore, much advancement in experimental and computational approaches has demonstrated entirely non‐cooperative (gradual) transitions via a continuum of states and a multitude of small energetic barriers between the N and U states of some proteins. These findings have been instrumental towards providing a structural rationale for cooperative versus noncooperative transitions, based on the coupling between interaction networks in proteins. The cooperativity inherent in a folding/unfolding reaction appears to be context dependent, and can be tuned via experimental conditions which change the stabilities of N and U. The evolution of cooperativity in protein folding transitions is linked closely to the evolution of function as well as the aggregation propensity of the protein. A large activation energy barrier in a fully cooperative transition can provide the kinetic control required to prevent the accumulation of partially unfolded forms, which may promote aggregation. Nevertheless, increasing evidence for barrier‐less “downhill” folding, as well as for continuous “uphill” unfolding transitions, indicate that gradual non‐cooperative processes may be ubiquitous features on the free energy landscape of protein folding.     

Phylogenetic Analysis: How Old are the Parts of Your Body?

According to the National Academy of Sciences, biology students in the USA are not being adequately prepared for successful futures. Of paramount concern is a lack of sufficient training in quantitative and computational skills, which are needed to compete effectively for an array of educational and occupational opportunities. In this paper, we introduce a classroom exercise that invites students to solve a simple biological problem and illustrates the need for a computer-assisted strategy to arrive at a solution. The exercise invites students to consider the question “How old are the parts of your body?” Some features of the human body are more ancient than others. For example, our bodies have both hair and backbones, but backbones arose much earlier in evolutionary history. Our exercise relies upon MEGA 4.0, a free, visually appealing, and intuitive computer program that allows students to gather DNA or protein sequences from electronic databases, then use them to infer phylogenetic trees. Student-inferred phylogenies are used to explore the relative order in which diverse aspects of the human form evolved. In the process, students are trained to use powerful features of MEGA and encouraged through group discussion to consider additional applications of the technology they have learned. Our lesson plan includes a brief video, a web site with essential terminology and links for further exploration, a hands-on experience using MEGA, and a follow-up discussion.     

How Tough are Sclerophylls?

Fracture toughness was estimated for a 'least tough' path inthe leaves of woody species from three sclerophyllous plantcommunities. Most of the species from Mediterranean, tropicalheath forest and lowland tropical rain forest habitats had verytough leaves, with toughness generally 600-1300 J m^-2, whichis two to four times higher than soft-leaved tropical pioneertrees. The toughest leaf (2032 J m^-2), Parishia insignis, camefrom the canopy of the lowland rain forest. Leaves from theshaded understorey of the rain forest did not appear any lesstough than those from the canopy.Copyright 1993, 1999 AcademicPress Leaf fracture toughness, sclerophylly, Mediterranean vegetation, tropical forest