Phylogenetic analysis reveals the surprising diversity of an oxygenase class

As metalloenzymes capable of transforming a broad range of substrates with high stereo- and regiospecificity, the multicomponent Rieske oxygenases (ROs) have been studied in bacterial systems for applications in bioremediation and industrial biocatalysis. These studies include genetic and biochemical investigations, determination of enzyme structure, phylogenetic analysis, and enzyme classification. Although RO terminal oxygenase components (RO–Os) share a conserved domain structure, their sequences are highly divergent and present significant challenges for identification and classification. Herein, we present the first global phylogenetic analysis of a broad range of RO–Os from diverse taxonomic groups. We employed objective, structure-based criteria to significantly reduce the inclusion of erroneously aligned sequences in the analysis. Our findings reveal that RO biochemical studies to date have been largely concentrated in an unexpectedly narrow portion of the RO–O sequence landscape. Additionally, our analysis demonstrates the existence two distinct groups of RO–O sequences. Finally, the sequence diversity recognized in this study necessitates a new RO–O classification scheme. We therefore propose a P450-like naming system. Our results reveal a diversity of sequence and potential catalytic functionality that has been wholly unappreciated in the RO literature. This study also demonstrates that many commonly used bioinformatic tools may not be sufficient to analyze the vast amount of data available in current databases. These findings facilitate the expanded exploration of RO catalytic capabilities in both biological and technological contexts and increase the potential for practical exploitation of their activities.     

Post-Haeckelian comparative biology — Adolf Naef’s idealistic morphology

Summary The present study describes the conceptual framework of Adolf Naef’s idealistic morphology as presented at the onset of the 20^th century. According to Naef, Haeckel’s and Gegenbaur’s approaches towards a phylogenetic biology were insufficient. He made it clear that Haeckel’s ideas were based on typological morphology. Thus, Haeckel’s views on comparative biology pointed back to pre-Darwinian concepts. Naef’s consequence was not to work out his own evolutionary morphology but to systematize the earlier typological concept. Consequently, he separated comparative morphology from phylogenetic studies. This idea was adopted by Hennig and was even imported into modern cladism.     

Micromechanics of smooth adhesive organs in stick insects: pads are mechanically anisotropic and softer towards the adhesive surface

Animals have evolved adhesive structures on their legs to cling to the substrate during locomotion. Here we characterise the ultrastructure and mechanical properties of adhesive pads in Carausius morosus (Phasmatodea) using atomic force microscopy (AFM) as well as transmission and scanning electron microscopy (TEM, SEM). The smooth adhesive arolium has a soft cuticle consisting of principal rods, which branch into finer fibres near the surface. Indentation experiments showed that the pad material consists of distinct layers with different mechanical properties. The 100–300 nm thick outermost layer consisting of the cuticulin envelope and the epicuticle is extremely soft and resilient (mean effective Young’s modulus 12 kPa), while the subjacent procuticle is a much stiffer material (mean effective Young’s modulus 625 kPa). AFM contact mode imaging revealed that the cuticle is mechanically anisotropic, which can be explained by its fibrillar inner structure. We propose that the described layered structure of smooth adhesive pads, consisting of materials decreasing in stiffness towards the outer surface, represents a superior design to conform and adhere to substrates with roughnesses at different length scales. This design principle could be easily implemented in technical adhesives, and thus has a potential to inspire biomimetic applications.     

A general definition of interpretation and its application to origin of life research

We draw on Short’s work on Peirce’s theory of signs to propose a new general definition of interpretation. Short argues that Peirce’s semiotics rests on his naturalised teleology. Our proposal extends Short’s work by modifying his definition of interpretation so as to make it more generally applicable to putatively interpretative processes in biological systems. We use our definition as the basis of an account of different kinds of misinterpretation and we discuss some questions raised by the definition by reference to parallel problems in the field of teleosemantics. We propose that interpretative responses fulfilling the criteria of our definition may be made by relatively simple molecular entities and we suggest two specific empirical applications of the definition to experimental work in the field of origin of life research. Our wider aim is to suggest that a well formulated naturalistic definition of interpretation will allow a re-evaluation of the role of semiotic phenomena in biological systems, including the generation of empirically testable hypotheses.     

The global evidence of early human symboling behaviour

A model of art origins based on the author’s first-hand studies is presented, which differs significantly from the dominant paradigm of these developments. The earliest known evidence for art, art-like or presumably non-utilitarian activities collectively provide the principal information about human symboling behaviour. These corpora are systematically considered from each continent, including rock art and various surviving forms of portable art. The immense age of some of this evidence is illuminated, and the record’s poor resolution with increasing age is presented as an essentially taphonomic phenomenon. It is shown, nevertheless, that the available record provides a considerably broader basis for hypotheses about symbolism, language and cognitive evolution than is often assumed, and that the evidence favours a model of comparatively early origins of the human capacity of concept-mediated thought and culture. These beginnings may be found in the endeavours of Lower Palaeolithic hominids to create taxonomic systems of physical reality. The available record renders it likely that such capacities existed several hundred thousand years ago.     

Change of the Protein p53 Electrochemical Signal According to its Structural Form – Quick and Sensitive Distinguishing of Native, Denatured, and Aggregated Form of the “Guardian of the Genome”

Presence of mutated and/or structurally modified (e.g., denatured, aggregated) protein p53 form is associated with several disorders such as Alzheimer’s disease, Parkinson’s disease, prion diseases, and many types of tumours. The aim of this work was to distinguish native, denatured and aggregated form of full-length p53 by flow injection analysis coupled with electrochemical detector (FIA-ED). Firstly FIA-ED method used for protein native form determination was optimized (detection limit 45.8 amol per 5 μl injection; 3×S/N). In addition the technique was applied to identify p53 structural forms (denatured and aggregated). It was found out that denatured form provides about three times higher electrochemical response (protein structure unfolding, approach of more electroactive centers – aminoacid residues – towards electrode surface) in comparison with native form. On the other hand, aggregated form offers lower response (steric eclipse of electroactive protein parts) when compared with the signal of native form. The obtained data show that we are not only able to sensitively determine native, denatured, and aggregated structural forms of p53 protein but also to distinguish them.     

Stationary multiple spots for reaction–diffusion systems

In this paper, we review analytical methods for a rigorous study of the existence and stability of stationary, multiple spots for reaction–diffusion systems. We will consider two classes of reaction–diffusion systems: activator–inhibitor systems (such as the Gierer–Meinhardt system) and activator–substrate systems (such as the Gray–Scott system or the Schnakenberg model). The main ideas are presented in the context of the Schnakenberg model, and these results are new to the literature. We will consider the systems in a two-dimensional, bounded and smooth domain for small diffusion constant of the activator. Existence of multi-spots is proved using tools from nonlinear functional analysis such as Liapunov–Schmidt reduction and fixed-point theorems. The amplitudes and positions of spots follow from this analysis. Stability is shown in two parts, for eigenvalues of order one and eigenvalues converging to zero, respectively. Eigenvalues of order one are studied by deriving their leading-order asymptotic behavior and reducing the eigenvalue problem to a nonlocal eigenvalue problem (NLEP). A study of the NLEP reveals a condition for the maximal number of stable spots. Eigenvalues converging to zero are investigated using a projection similar to Liapunov–Schmidt reduction and conditions on the positions for stable spots are derived. The Green’s function of the Laplacian plays a central role in the analysis. The results are interpreted in the biological, chemical and ecological contexts. They are confirmed by numerical simulations.      

Mutant Bacteriophages,Frank Macfarlane Burnet,and the Changing Nature of “Genespeak” in the 1930s

In 1936, Frank Macfarlane Burnet published a paper entitled “Induced lysogenicity and the mutation of bacteriophage within lysogenic bacteria,” in which he demonstrated that the introduction of a specific bacteriophage into a bacterial strain consistently and repeatedly imparted a specific property – namely the resistance to a different phage – to the bacterial strain that was originally susceptible to lysis by that second phage. Burnet’s explanation for this change was that the first phage was causing a mutation in the bacterium which rendered it and its successive generations of offspring resistant to lysogenicity. At the time, this idea was a novel one that needed compelling evidence to be accepted. While it is difficult for us today to conceive of mutations and genes outside the context of DNA as the physico-chemical basis of genes, in the mid 1930s, when this paper was published, DNA’s role as the carrier of hereditary information had not yet been discovered and genes and mutations were yet to acquire physical and chemical forms. Also, during that time genes were considered to exist only in organisms capable of sexual modes of replication and the status of bacteria and viruses as organisms capable of containing genes and manifesting mutations was still in question. Burnet’s paper counts among those pieces of work that helped dispel the notion that genes, inheritance and mutations were tied to an organism’s sexual status. In this paper, I analyze the implications of Burnet’s paper for the understanding of various concepts – such as “mutation,” and “gene,” – at the time it was published, and how those understandings shaped the development of the meanings of these terms and our modern conceptions thereof.     

Question 7: Modelling Minimal ‘Lipid-Peptide’ Cells

This contribution is aimed to give support to ‘bottom-up’ approaches to the minimal or early cell research project. Even if, from this perspective, the most simple living cell still seems very far away, the analysis of less complex, infrabiological cellular systems (some of which could be relatively soon implemented in the lab) probably holds the key, or one of the fundamental keys, to the problem of origins of life. On these lines, we propose a simulation model to study the transition from proto-metabolic ‘lipid’ cells to ‘lipid-peptide’ cells, as a critical step in which self-reproducing vesicles could develop into more functionalized supramolecular systems Presented at: International School of Complexity – 4th Course: Basic Questions on the Origins of Life; “Ettore Majorana” Foundation and Centre for Scientific Culture, Erice, Italy, 1–6 October 2006.     

Methods to classify familial relationships in the presence of laboratory errors, without parental data

We consider the problem of accurate classification of family relationship in the presence of laboratory error without parental data. We first propose an adjusted version of the test statistic proposed by Ehm and Wagner based on the summation over a large number of genetics markers. We then propose use of the Bayes factor as a classification rule. We prove theoretically that the Bayes factor is the optimal classification rule in that the total classification error is minimized. We show via simulations that both the adjusted Ehm and Wagner method and Bayes factor classification rule reduce misclassification errors, and that the Bayes factor classification rule is robust against under-estimation or over-estimation of laboratory errors. For monozygotic twins versus dizygotic twins, the correct classification rate of the Bayes rule is over 99%. For full-siblings versus half-siblings, the Bayes factor classification rule generally outperforms Ehm and Wagner’s method (in Am J Hum Genet 62:181–188, 1998), especially when full-sibling proportion is high.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

A comparison of national approaches to setting ecological status boundaries in phytobenthos assessment for the European Water Framework Directive: results of an intercalibration exercise

The European Union (EU)’s Water Framework Directive (WFD) requires that all Member States participate in intercalibration exercises in order to ensure that ecological status concepts and assessment levels are consistent across the EU. This paper describes one such exercise, performed by the countries in the Central/Baltic Geographical Intercalibration Group stretching from Ireland in the west to Estonia in the east and from the southern parts of Scandinavia to the northern regions of Spain and Italy (but excluding alpine regions, which were intercalibrated separately). In this exercise, methods used to measure ecological status of rivers using benthic diatoms were compared. Ecological status is estimated as the ratio between the observed value of a biological element and the value expected in the absence of significant human impact. Approaches to defining the ‘reference sites’, from which these ‘expected’ values were derived, varied from country to country. Minimum criteria were established as part of the exercise but there was still considerable variation between national reference values, reflecting typological differences that could not be resolved during the exercise. A simple multimetric index was developed to compare boundary values using two widely used diatom metrics. Boundary values for high/good status and good/moderate status set by each participant were converted to their equivalent values of this intercalibration metric using linear regression. Variation of ±0.05 EQR units around the median value was considered to be acceptable and the exercise provided a means for those Member States who fell significantly above or below this line to review their approaches and, if necessary, adjust their boundaries. Handling editor: J. Padisak     

Phylogeography of the endemic St. Lucia whiptail lizard Cnemidophorus vanzoi: Conservation genetics at the species boundary

Vicariance and isolation leading to speciation of reptiles on islands is well exemplified in a number of taxa in the Caribbean. The St. Lucia whiptail (Cnemidophorus vanzoi), considered a single species, is found on two small islets (Maria Major and Maria Minor) off the main island of St. Lucia. From lizards collected from both localities, we gathered morphological measurements and analysed the genetic divergence between populations, using a molecular survey of ∼ ∼2800 mtDNA base pairs and 8 microsatellites. There are significant differences in body size and general form and fixed but small mtDNA differences between island populations. Microsatellites reveal low diversity within populations but very high differentiation between islands with non-overlapping allele size ranges at all except one microsatellite and two loci exhibiting single-base polymorphism, fixed between islands. Based on these results, we examine published criteria to determine whether the studied island forms could be considered true species. According to the phylogenetic species concept and Moritz’s evolutionary significant unit (ESU) criteria, the two lizard populations can be considered separate entities. Crandall et al.’s (2000, Trends Ecol. Evol., 15, 290–295) broader categorization of population distinctiveness, based on concepts of ecological and genetic exchangeability, produces conflicting results depending on the interpretation of the observed ecological data. Following Fraser and Bernatchez’s (2001, Mol. Ecol., 10, 2741–2752) framework for management decisions when ecological data are not sufficient we propose that the lizard populations on the Maria islands are on differing evolutionary trajectories and thus at the species boundary. The populations are of high priority to conservation, thus meriting separate management.     

RAPD Fingerprint to Appraise the Genetic Fidelity of In Vitro Propagated <Emphasis Type="Italic">Araucaria excelsa</Emphasis> R. Br. var. glauca Plantlets

Randomly amplified polymorphic DNA (RAPD) was used as a tool to assess the genetic fidelity of in vitro propagated Araucaria excelsa R. Br. var. glauca with explants taken from orthotropic stem along with their related mother plants after treatment with kinetin, 2iP, BA (0.02–0.26 mg/l) and TDZ (0.001–1 mg/l) to produce axillary shoots. TDZ and kinetin induced more shoot and higher length per explant. Results showed a total of 1,676 fragments were generated with 12 RAPD primers in micropropagated plants and their donor mother plants. The number of loci ranged from 6 in OPB 12–18 in OPY 07 with a size ranging from 250 bp in OPH 19–3500 bp in OPH 11. Cluster analysis of RAPD data using UPGMA (unweighted pair group method with arithmetic average) revealed more than 92% genetic similarities between tissue cultured plants and their corresponding mother plant measured by the Jaccard’s similarity coefficient. Similarity matrix and PCoA (two dimensional principal coordinate analysis) resulted in the same affinity. Primers had shown 36% polymorphism. However, careful monitoring of tissue culture derived plants might be needed to determine that rooted shoots are adventitious in origin.     

Preformulation Considerations for Controlled Release Dosage Forms: Part I Selecting Candidates

The physical–chemical properties of interest for Controlled Release (CR) dosage form development presented are based on the author’s experience. Part I addresses selection of the final form based on a logical progression of physical–chemical properties evaluation of candidate forms and elimination of forms with undesirable properties from further evaluation in order to simplify final form selection. Several candidate forms which could include salt, free base or acid, polymorphic and amorphic forms of a new chemical entity (NCE) or existing drug substance (DS) are prepared and evaluated for critical properties in a scheme relevant to manufacturing processes, predictive of problems, requiring small amounts of test materials and simple analytical tools. A stability indicating assay is not needed to initiate the evaluation. This process is applicable to CR and immediate release (IR) dosage form development. The critical properties evaluated are melting, crystallinity, solubilities in water, 0.1 N HCl, and SIF, hygrodymamics, i.e., moisture sorption and loss at extremes of RH, and LOD at typical wet granulation drying conditions, and processability, i.e., corrosivity, and filming and/or sticking upon compression. Presented at the 41st Annual Pharmaceutical Technologies Arden Conference—Oral Controlled Release Development and Technology, January 2006, West Point, NY.     

Simple testing procedures for the Holling type II model

In this paper, we consider predator–prey data that can be viewed as solutions to a planar system of ordinary differential equations (ODE) observed with random error. The ODE system admits a limit cycle, while the random error is supposed to act additively in the log-scale. One of the oldest such systems is Holling’s type II model. In spite of its simplicity, it is still very popular in data analyses, although more sophisticated models have been introduced in the literature. We propose a simple way of deciding whether a set of predator–prey pairs is indicative or not of a departure from this basic model by exploiting the geometric properties of the solution in the phase plane. To illustrate our method, we use simulated and real data.     

Size doesn’t matter: towards a more inclusive philosophy of biology

Philosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations.     

The role of herbivorous water birds in aquatic systems through interactions with aquatic macrophytes,with special reference to the Bewick’s Swan – Fennel Pondweed system

The role of aquatic macrophytes in stimulating biodiversity and maintaining clear waters is currently undisputed. The management of (eutrophic) shallow waters is therefore often directed at (re-)establishing macrophyte domination. In contrast, the role of water birds has long been considered of minor importance for the functioning of fresh water ecosystems. Indeed, in terms of biomass and production, water birds constitute only a minor part of these systems. However, water birds may graze heavily on water plants under certain circumstances, and the question arises whether herbivorous water birds have an important indirect effect on shallow fresh water systems. Mainly illustrated with the interaction between Bewick’s Swans and Fennel Pondweed, we present data on the role that water plants may play in the life of water birds and how water birds may impact water plants’ fitness in terms of survival, production, dispersal and competitive ability. It appears that water plants may be crucial for water birds during periods of high-energy requirements, such as migration. Despite the plants’ costs associated with water bird grazing, the interaction between water birds and water plants varies in nature from an apparent predator–prey relationship to a mutually beneficial interaction depending on the context and the perspective. For the case of the Bewick’s Swan–Fennel Pondweed interaction, regular bird grazing is sustainable and may actually favour the plant’s dispersal. Thus, Bewick’s Swans themselves may in fact play a crucial role in establishing and maintaining the Fennel Pondweed rich staging sites between the swans’ wintering and breeding grounds, which are vital for the swans’ successful migration.     

Genes and the Environment in Neurodegeneration

Neurodegenerative diseases are a heterogeneous group of pathologies which includes complex multifactorial diseases, monogenic disorders and disorders for which inherited, sporadic and transmissible forms are known. Factors associated with predisposition and vulnerability to neurodegenerative disorders may be described usefully within the context of gene–environment interplay. There are many identified genetic determinants for neurodegeneration, and it is possible to duplicate many elements of recognized human neurodegenerative disorders in animal models of the disease. However, there are similarly several identifiable environmental influences on outcomes of the genetic defects; and the course of a progressive neurodegenerative disorder can be greatly modified by environmental elements. In this review we highlight some of the major neurodegenerative disorders (Alzheimer’s disease, Parkinson’s disease, Amyotrophic lateral sclerosis, Huntington’s disease, and prion diseases.) and discuss possible links of gene–environment interplay including, where implicated, mitochondrial genes.