Eukaryotic systematics: a user's guide for cell biologists and parasitologists

Single-celled parasites like Entamoeba, Trypanosoma, Phytophthora and Plasmodium wreak untold havoc on human habitat and health. Understanding the position of the various protistan pathogens in the larger context of eukaryotic diversity informs our study of how these parasites operate on a cellular level, as well as how they have evolved. Here, we review the literature that has brought our understanding of eukaryotic relationships from an idea of parasites as primitive cells to a crystallized view of diversity that encompasses 6 major divisions, or supergroups, of eukaryotes. We provide an updated taxonomic scheme (for 2011), based on extensive genomic, ultrastructural and phylogenetic evidence, with three differing levels of taxonomic detail for ease of referencing and accessibility (see supplementary material at Cambridge Journals On-line). Two of the most pressing issues in cellular evolution, the root of the eukaryotic tree and the evolution of photosynthesis in complex algae, are also discussed along with ideas about what the new generation of genome sequencing technologies may contribute to the field of eukaryotic systematics. We hope that, armed with this user's guide, cell biologists and parasitologists will be encouraged about taking an increasingly evolutionary point of view in the battle against parasites representing real dangers to our livelihoods and lives.     

Paraphyly of the Pseudophyllidea (Platyhelminthes: Cestoda): circumscription of monophyletic clades based on phylogenetic analysis of ribosomal RNA

Phylogenetic relationships of cestodes of the order Pseudophyllidea (Platyhelminthes: Cestoda) were examined using sequences of complete small subunit and partial (D1-D3 region) large subunit nuclear rDNA of members of all pseudophyllidean families. The results provide evidence of paraphyly of the order as indicated by previous molecular phylogenetic analyses based on a much lower number of species sequenced. Pseudophyllidean tapeworms represent an artificial assemblage comprising two unrelated clades. “Bothriocephalidea” is formed by four families sensu Bray et al. (1994), namely Bothriocephalidae, Echinophallidae, Philobythiidae and Triaenophoridae, whereas two other families, Diphyllobothriidae and Cephalochlamydidae, give rise to the “Diphyllobothriidea”. The present results indicate that “Bothriocephalidea” forms the most derived clade of all difossate and tetrafossate/bothriate tapeworm lineages which are considered to be basal relative to the rest of tetrafossate/bothridiate and acetabulate cestodes. By contrast, “Diphyllobothriidea”, which includes medically important parasites (Diphyllobothrium and Spirometra), appeared more basal, without a clearly resolved position within other difossate tapeworm lineages.     

Old trees, new trees--is there any progress?

The amount of comparative data for phylogenetic analyses is constantly increasing. Data come from different directions such as morphology, molecular genetics, developmental biology and paleontology. With the increasing diversity of data and of analytical tools, the number of competing hypotheses on phylogenetic relationships rises, too. The choice of the phylogenetic tree as a basis for the interpretation of new data is important, because different trees will support different evolutionary interpretations of the data investigated. I argue here that, although many problematic aspects exist, there are several phylogenetic relationships that are supported by the majority of analyses and may be regarded as something like a robust backbone. This accounts, for example, for the monophyly of Metazoa, Bilateria, Deuterostomia, Protostomia (= Gastroneuralia), Gnathifera, Spiralia, Trochozoa and Arthropoda and probably also for the branching order of diploblastic taxa (“Porifera”, Trichoplax adhaerens, Cnidaria and Ctenophora). Along this “backbone”, there are several problematic regions, where either monophyly is questionable and/or where taxa “rotate” in narrow regions of the tree. This is illustrated exemplified by the probable paraphyly of Porifera and the phylogenetic relationships of basal spiralian taxa. Two problems span wider regions of the tree: the position of Arthropoda either as the sister taxon of Annelida (= Articulata) or of Cycloneuralia (= Ecdysozoa) and the position of tentaculate taxa either as sister taxa of Deuterostomia (= Radialia) or within the taxon Spiralia. The backbone makes it possible to develop a basic understanding of the evolution of genes, molecules and structures in metazoan animals.     

Detectability and criterion measures in temporal generalization

Computer simulation of performance on “normal” and “episodic” temporal generalization tasks was used to examine the relations between the theoretical parameters of models which fit temporal generalization data (“timing sensitivity” and “threshold”), and the d′ (detectability) and beta (decision criterion) measures of signal-detection theory. In general, changes in timing sensitivity altered d′, whereas threshold changes affected beta, supporting the assertion that the two sorts of variables (“sensitivity/detectability” and “threshold/criterion”) were psychologically equivalent. Cases where temporal generalization gradients were apparently contaminated by “random responding” could be treated by changes in beta, but cases in which temporal generalization gradients were not peaked at the standard posed severe problems for a simple signal-detection account, although existing models of temporal generalization performance could deal with them.     

Combining theoretical and experimental approaches to understand the circadian clock

This review is intended as a summary of our work carried out as part of the German Research Association (DFG) Center Program on Circadian Rhythms. Over the last six years, our approach to understanding circadian systems combined theoretical and experimental tools, and Gonyaulax and Neurospora have proven ideal for these efforts. Both of these model organisms demonstrate that even simple circadian systems can have multiple light input pathways and more than one rhythm generator. They have both been used to elaborate basic circadian features in conjunction with formal models. The models introduce the “zeitnehmer,” i.e., a clock-regulated input pathway, to the conceptual framework of circadian systems, and proposes networks of individual feedbacks as the basis for circadian rhythmicity.     

Modelling the microenvironment of a lipase immobilized in polyurethane foams

The effects of partition of substrates and product on the modelling of the microenvironment of an immobilized lipase were evaluated using Response Surface Methodology. The esterification of butyric acid with ethanol in n-hexane, catalyzed by Candida rugosa lipase immobilized in two biocompatible and relatively hydrophilic polyurethane foams (“Hypol FHP 2002™” and “Hypol FHP 5000™”) was used as the model system. For each set of initial conditions, the final concentration of substrates and ethyl butyrate in the microenvironment, at equilibrium, Cmicro, were estimated by mass balancing bulk and foams. The Cmicro values obtained were used to estimate the corresponding partition coefficients of ethanol (P_EtOH), butyric acid (P_BA) and ester (P_EB), between the foams (microenvironment) and the bulk medium. Foams containing previously inactivated lipase, as well as lipase-free foams were used. For both substrates, Cmicro values were, in the majority of the experiments, higher than their macroenvironmental counterparts. The lowest Cmicro values were observed with the less hydrophilic foam (“FHP 5000”). A decrease of Cmicro_EtOH in both foams and Cmicro_BA in “FHP 5000” foams, was obtained upon lipase immobilization. P_EB values were, in all cases, close to zero. This is beneficial in terms of the shift in reaction equilibrium, product recovery and alleviation of product inhibition effects.     

Alternate histories of cytokinesis: lessons from the trypanosomatids

Popular culture has recently produced several “alternate histories” that describe worlds where key historical events had different outcomes. Beyond entertainment, asking “could this have happened a different way?” and “what would the consequences be?” are valuable approaches for exploring molecular mechanisms in many areas of research, including cell biology. Analogous to alternate histories, studying how the evolutionary trajectories of related organisms have been selected to provide a range of outcomes can tell us about the plasticity and potential contained within the genome of the ancestral cell. Among eukaryotes, a group of model organisms has been employed with great success to identify a core, conserved framework of proteins that segregate the duplicated cellular organelles into two daughter cells during cell division, a process known as cytokinesis. However, these organisms provide relatively sparse sampling across the broad evolutionary distances that exist, which has limited our understanding of the true potential of the ancestral eukaryotic toolkit. Recent work on the trypanosomatids, a group of eukaryotic parasites, exemplifies alternate historical routes for cytokinesis that illustrate the range of eukaryotic diversity, especially among unicellular organisms.     

Evolution of the mitochondrial genome: protist connections to animals, fungi and plants

The past decade has seen the determination of complete mitochondrial genome sequences from a taxonomically diverse set of organisms. These data have allowed an unprecedented understanding of the evolution of the mitochondrial genome in terms of gene content and order, as well as genome size and structure. In addition, phylogenetic reconstructions based on mitochondrial DNA (mtDNA)-encoded protein sequences have firmly established the identities of protistan relatives of the animal, fungal and plant lineages. Analysis of the mtDNAs of these protists has provided insight into the structure of the mitochondrial genome at the origin of these three, mainly multicellular, eukaryotic groups. Further research into mtDNAs of taxa ancestral and intermediate to currently characterized organisms will help to refine pathways and modes of mtDNA evolution, as well as provide valuable phylogenetic characters to assist in unraveling the deep branching order of all eukaryotes.     

Cochliopodium barki n. sp. (Rhizopoda, Himatismenida) re-isolated from soil 30 years after its initial description

A strain of Cochliopodium isolated from grassland soil at Sourhope Research Station (Scotland, UK) was found to be identical to the strain “Cochliopodium sp.2” studied by Bark in 1973. We name it Cochliopodium barki. It belongs to a group of species (comprising also C. minus and Cochliopodium sp. “NYS strain”) with very similar scale pattern.     

Quantitative techniques for steady-state calculation and dynamic integrated modelling of membrane potential and intracellular ion concentrations

The membrane potential (E_m) is a fundamental cellular parameter that is primarily determined by the transmembrane permeabilities and concentration gradients of various ions. However, ion gradients are themselves profoundly influenced by E_m due to its influence upon transmembrane ion fluxes and cell volume (V_c). These interrelationships between E_m, V_c and intracellular ion concentrations make computational modelling useful or necessary in order to guide experimentation and to achieve an integrated understanding of experimental data, particularly in complex, dynamic, multi-compartment systems such as skeletal and cardiac myocytes. A variety of quantitative techniques exist that may assist such understanding, from classical approaches such as the Goldman–Hodgkin–Katz equation and the Gibbs–Donnan equilibrium, to more recent “current-summing” models as exemplified by cardiac myocyte models including those of DiFrancesco & Noble, Luo & Rudy and Puglisi & Bers, or the “charge-difference” modelling technique of Fraser & Huang so far applied to skeletal muscle. In general, the classical approaches provide useful and important insights into the relationships between E_m, V_c and intracellular ion concentrations at steady state, providing their core assumptions are fully understood, while the more recent techniques permit the modelling of changing values of E_m, V_c and intracellular ion concentrations. The present work therefore reviews the various approaches that may be used to calculate E_m, V_c and intracellular ion concentrations with the aim of establishing the requirements for an integrated model that can both simulate dynamic systems and recapitulate the key findings of classical techniques regarding the cellular steady state. At a time when the number of cellular models is increasing at an unprecedented rate, it is hoped that this article will provide a useful and critical analysis of the mathematical techniques fundamental to each of them.     

Sphenophyllum miravallis Vetter and Bowmanites cupulatus sp.n. from the “Illinger Flözzone” (“Heusweiler Schichten”, Lower Stephanian, Saar Basin, German Federal Republic)

This paper deals with a detailed study of Sphenophyllum miravallis Vetter, a member of the “Sphenophyllum thonii group”. New material from the Reisbach colliery, working the “Illinger Flözzone” of the “Heusweiler Schichten” (Lower Stephanian, Saar Basin, German Federal Republic), is described morphologically and anatomically, and the species is discussed. The new material enlarges the known range of variability of the normal aspect of the foliage, i.e. the foliage of the thinner branches. Thicker stems with their aberrant polymorphous foliage, and cellular details, are described for the first time. An emended diagnosis is given. Comparisons with other species are made.

The new species Bowmanites cupulatus is introduced to accommodate fructufications most probably belonging to Sphenophyllum miravallis.

S. crenulatum Knight ex Wagner is considered to be a heterotypic synonym of S. miravallis, the latter name having priority.     

Contribution of response surface design to the development of glycerolysis systems catalyzed by commercial immobilized lipases

Two commercial immobilized lipases (“Lipozyme® IM” and “Novozym® 435”) were tested as biocatalysts for the glycerolysis of olive residue oil in n-hexane aimed at the production of monoglycerides (MG) and diglycerides (DG). A central composite rotatable design (CCRD) was followed to model and optimize glycerolysis as a function of both the amount of biocatalyst (L) and of the molar ratio glycerol/triglycerides (Gly/TG). For both biocatalysts, the production of free fatty acids (FFA) was described by second order models. In terms of MG and DG production, as well as of TG conversion, the best fits were obtained with first-order models. The highest MG productions were in the range 43–45% (w/w, on the basis of total fat) for both biocatalysts tested at a (Gly/TG) ratio of one. In the case of “Novozym 435”, the lowest load used (12%, w/w) gave the best results, in contrast with “Lipozyme IM” with which a concentration of about 26% (w/w) was necessary to obtain the highest production. Under these conditions, the amount of FFA produced was about 2% and 10% (w/w), respectively, for “Novozym 435” and “Lipozyme IM” catalyzed systems. Considering both FFA production and lipase loading, “Novozym 435” was shown to be a better biocatalyst for the glycerolysis of olive residue oil in n-hexane, aimed at the production of MG, than “Lipozyme IM”.     

Macroscopic electrical activity as a conceptual framework in cognitive neuroscience

This report has the aim to indicate relevant implications of the systems theory approach to the experiments in conscious brain. The reports related to comparative neurophysiology and to the understanding of brain as a “whole” are rare, an outstanding comparative approach report in biological sciences was that of Darwin, who performed a voyage in order to compare structures of species and the principle of natural selectivity.

In despite of the fruitful approach of Darwin, most of the brain scientists do prefer to analyze either one type of brain or even only one structure to interpret the brain function. The single neuron doctrine developed by Sherrington also did not consider these various aspects. The avenue opened by Hans Berger which introduced the analysis of the brain oscillations was an important step towards understanding of the “whole brain”.

In this report we aim to describe narratively, technical, strategical and philosophical steps to bridge “Sherrington Neuron Doctrine” with the “Neurons-Brain Theory” of the whole brain by means of the method developed by Hans Berger.     

Laser-induced reactions of P700 and cytochrome f in a blue-green alga, Plectonema boryanum

Kinetics of the absorption change of P700 (blue band) and cytochrome f in whole cells of a blue-green alga, Plectonema boryanum, have been studied by Q-switched ruby-laser flash excitation (694 nm; approx. 20 nsec) to elucidate the sequential relationship of these two components in photosynthetic electron transport. “P700” was photooxidized within 2 μsec and recovered in two phases t_1/2 10 μsec and 200 μsec). Under the same conditions cytochrome f was oxidized with a half time of 15 μsec. The magnitude of the fast phase of “P700” recovery, however, diminished at lower laser intensity while the cytochrome f change remained unaffected. The result suggests that cytochrome f and P700 may not be on the same electron-transport chain.     

Aspects of permian palaeobotany and palynology. III. A new reconstruction of Lilpopia raciborskii (Lilpop) conert et schaarschmidt (Sphenopsida)

The early Permian plant Lilpopia raciborskii (Sphenopsida) has been found for the first time outside its type region, the Karniowice area (Poland). On the basis of this new material, collected in the “Waderner Gruppe” of Sobernheim (Nahe area, German Federal Republic), L. raciborskii is described and discussed in the light of previous concepts of this species; a new and more complete reconstruction of the taxon is presented. For the first time epidermal features are described. The heterophyllous leaves of L. raciborskii are compared with Sphenophyllum thonii var. minor Sterzel.     

The effect of infra-red radiation on rectal temperature and respiration rate of unacclimated female new zealand white rabbits

1. 1.|An experiment was carried out to examine the effects of various levels of infra-red (i.r.) radiation on rectal temperature (RT) and respiration rate (RR) in New Zealand While rabbits.

2. 2.|A 4 × 3 × 6 factorial design was employed in which the factors were: four intensities of i.r. radiant heating of 0.0, 1.9, 2.1 and 2.4 MJ/m²/h, three replicates and six rabbits.

3. 3.|rectal temperature differed (P < 0.05) between treatments and were highest at the “high” level of i.r. radiation (1°C higher than for controls). At the “medium” and “low” levels of i.r. heating RTs were respectively 0.3 and 0.2°C higher than in controls.

4. 4.|At different levels of radiation RR were different (P < 0.05), with the highest (422.7 ± 218.1 breaths/min) at 2.4 MJ/m²/h i.r. radiant heating. This RR was almost 2.5 times that in controls, while at the “low” and “medium” i.r. levels RR values were respectively 1.5 and 2 times those of controls.

Phenolic acids and resistance to insect attack in Sorghum bicolor

Glucose and quinic acid esters of several hydroxybenzoic and cinnamic acids were identified in methanolic extracts of leaves of 15-day-old Sorghum bicolor together with two O-glucosides. Some of the phenolic acids were also found to occur as insoluble esters of cell wall polysaccharides. While these derivatives did not affect the feeding of Locusta migratoria on sorghum, the free acids, as a mixture, were markedly inhibitory. It was found that Sorghum contained a mixture of hydrolases which could effect the transformation of “inactive” phenolic esters and glycosides into “active” phenolic acids at a high enough concentration to significantly reduce feeding by Locusta.     

What can biological barcoding do for marine biology?

The idea of using nucleotide sequences as barcodes for species identification has stirred up debates in the community of taxonomists and systematists. We argue that barcodes are potentially extremely useful tools for taxonomy for several reasons. Barcodes may, for example, help to identify cryptic and polymorphic species and give means to associate life history stages of unknown identity. Barcode systems would thus be particularly helpful in cases when morphology is ambiguous or uninformative and would provide tools for higher taxonomic resolution of disparate life forms. Comparative analysis of short DNA sequences may also represent heuristic access cards to a deeper understanding of evolutionary relationships between organisms. However, barcodes are the “essence” of species identities no more than taxonomic holotypes are “the species”. It makes no sense to think that morphology and other biological information about organisms can be made obsolete by barcode systems. The biological significance of matching or diverging nucleotide sequences will still have to be the subject of taxonomic decisions that must be open for scrutiny. It is imperative, therefore, that barcodes are associated with specimen vouchers.