On a possible relationship between bacterial endospore formation and the origin of eukaryotic cells

The acquisition of intracellular organelles, including mitochondria and plastids and a membrane-bounded nucleus, have been postulated to be key events in the development of the eukaryotic from the prokaryotic ancestral cell. The two major hypotheses to account for such acquisitions are: (1) primitive cells originally obtained organelles by engulfing free-living prokaryotes which then entered into symbiotic association (“endosymbiosis”) with them; (2) organelles arose through the engulfment by the primitive cell of part of its own cytoplasm. To some extent, the former hypothesis has received most support, because endosymbiosis is known to occur in extant organisms, whilst the latter hypothesis has received less support, because cytoplasmic engulfment by prokaryotes is not now thought to occur. However, during the process of endospore formation by extant bacteria, the protoplast within the single cell is observed to divide in a unique manner such that the cell in effect engulfs a portion of its own cytoplasm. The process is strikingly similar to the engulfment suggested by the second hypothesis to have initiated the evolution of eukaryotes. The engulfed cytoplasm is bounded by a double membrane within the “mother cell” and contains enzymes, ribosomes and a complete genome. In many respects this parallels the supposed primitive eukaryotic state and, it is argued, confers potential advantages on the cell, particularly through the control that the “mother cell” can exert on the enclosed compartment. It is hypothesized that bacterial endospore formation is therefore one product of evolution from an early engulfment event that led also to the development of complex eukaryotic cells.     

Peroxisomes, glyoxysomes and glycosomes (review)

Peroxisomes, glyoxysomes and glycosomes are related organelles found in different organisms. The morphology and enzymic content of the different members of this organelle family differ considerably, and may also be highly dependent on the cell's environmental conditions or life cycle. However, all peroxisome-like organelles have in common a number of characteristic enzymes or enzyme systems, notably enzymes dealing with reactive oxygen species. All organelles of the family follow essentially the same route of biogenesis, but with species-specific differences. Sets of proteins called peroxins are involved in different aspects of the formation and proliferation of peroxisomes such as import of proteins in the organellar matrix, insertion of proteins in the membrane, etc. In different eukaryotic lineages these functions are carried out by often--but not always--homologous yet poorly conserved peroxins. The process of biogenesis and the nature of the proteins involved suggest that all members of the peroxisome family evolved from a single organelle in an ancestral eukaryotic cell. This original peroxisome was possibly derived from a cellular membrane system such as the endoplasmic reticulum. Most of the organism-specific functions of the extant organelles have been acquired later in evolution.     

Peroxisomes,glyoxysomes and glycosomes (Review)

Peroxisomes, glyoxysomes and glycosomes are related organelles found in different organisms. The morphology and enzymic content of the different members of this organelle family differ considerably, and may also be highly dependent on the cell's environmental conditions or life cycle. However, all peroxisome-like organelles have in common a number of characteristic enzymes or enzyme systems, notably enzymes dealing with reactive oxygen species. All organelles of the family follow essentially the same route of biogenesis, but with species-specific differences. Sets of proteins called peroxins are involved in different aspects of the formation and proliferation of peroxisomes such as import of proteins in the organellar matrix, insertion of proteins in the membrane, etc. In different eukaryotic lineages these functions are carried out by often – but not always – homologous yet poorly conserved peroxins. The process of biogenesis and the nature of the proteins involved suggest that all members of the peroxisome family evolved from a single organelle in an ancestral eukaryotic cell. This original peroxisome was possibly derived from a cellular membrane system such as the endoplasmic reticulum. Most of the organism-specific functions of the extant organelles have been acquired later in evolution.     

Evolution of the chaperonin families (HSP60, HSP 10 and TCP-1) of proteins and the origin of eukaryotic cells

The members of the 10 kDa and 60 kDa heat-shock chaperonin proteins (Hsp10 and Hsp60 or Cpn10 and Cpn60), which form an operon in bacteria, are present in all eubacteria and eukaryotic ceil organelles such as mitochondria and chloroplasts. In archaebacteria and eukaryotic cell cytosol, no close homologues of Hsp10 or Hsp60 have been identified. However, these species (or ceil compartments) contain the Tcp-1 family of proteins (distant homologues of Hsp60). Phylogenetic analysis based on global alignments of Hsp60 and Hsp10 sequences presented here provide some evidence regarding the evolution of mitochondria from a member of the α-subdivision of Gram-negative bacteria and chloroplasts from cyanobacterial species, respectively. This inference is strengthened by the presence of sequence signatures that are uniquely shared between Hsp60 homologues from α-purple bacteria and mitochondria on one hand, and the chloroplasts and cyanobacterial hsp60s on the other. Within the α-purple subdivision, species such as Rickettsia and Ehrlichia, which live intracellularly within eukaryotic cells, are indicated to be the closest relatives of mitochondrial Homologues, In the Hsp60 evolutionary tree, rooted using the Tcp-1 homologue, the order of branching of the major groups was as follows: Gram-positive bacteria — cyanobacteria and chloroplasts — chlamydiae and spirochaetes —β and γ-Gram-negative purple bacteria —α-purple bacteria — mitochondria. A similar branching order was observed independently in the Hsp10 tree. Multiple Hsp60 homologues, when present in a group of species, were found to be clustered together in the trees, indicating that they evolved by independent gene-duplication events. This review also considers in detail the evolutionary relationship between Hsp50 and Tcp-1 families of proteins based on two different models (viz. archaebacterial and chimeric) for the origin of eukaryotic cell nucleus. Some predictions of the chimeric model are also discussed.     

Zinc transporters and the cellular trafficking of zinc

Zinc is an essential nutrient for all organisms because this metal serves as a catalytic or structural cofactor for many different proteins. Zinc-dependent proteins are found in the cytoplasm and within many organelles of the eukaryotic cell including the nucleus, the endoplasmic reticulum, Golgi, secretory vesicles, and mitochondria. Thus, cells require zinc transport mechanisms to allow cells to efficiently accumulate the metal ion and distribute it within the cell. Our current knowledge of these transport systems in eukaryotes is the focus of this review.     

The Invasive Nature of an Infectious Bacterial Symbiont

ABSTRACT. Xenosomes are infectious bacterial symbionts that exist exclusively in the cytoplasm of the small philasterine marine ciliate Parauronema acutum. We have used this host-symbiont system as a model to study infection. In the past we postulated that infection took place by a process in which the symbionts escaped digestion and entered into the host's cytoplasm through the food vacuole during phagocytosis. This is clearly not the case. We now present evidence based on electron microscopic observations that the symbionts infect in a manner involving direct penetration of the protozoan's cell membranes. We have obtained additional data that suggest that, following entrance of the symbionts into the cytoplasm, only a single xenosome is required to establish an infection.     

Selektion und Evolutionstheorie: Müssen »altdarwinistische Dogmen« durch eine kritische Evolutionstheorie ersetzt werden?

Some authors (mainlyBonik, Gutmann, andPeters) have tried to revise current evolutionary concepts, fraught — in their opinion — with “1paleodarwinistic dogmas”. Some points of their theories are reviewed critically in the present paper: (1) Evolution is of course inimaginable without selection, but an “internal selection” eliminating misshaped embryos has nothing to do with evolution. This is stabilizing selection which reduces genetic variation and would even block evolutionary change completely if it was perfect. When this kind of internal selection was “neglected” by earlier authors, this cannot be qualified as paleodarwinistic dogmatism being in contradiction with the premises of evolutionary theory. — (2) Energetic rationalisation of organisms is certainly an important factor in selection but not an absolute law explaining everything about evolution. There are many adaptive processes resulting in less “economic” formations; e.g. heavy armors like those of tortoises, ankylosaurs, and stegosaurs. Among others, protective functions justify a certain waste of energy. — (3) Comparing organisms with technical machines provides an interesting analogy, but again this cannot be considered as the only possible approach for evolutionary models. »Maschinenanalogie« combined with a generalized »internal selection« (i.e. with the nature of adaptive changes determined by the internal construction of organisms) leads inevitably to an underestimation of selective pressures resulting from the ecologic and biocoenotic context. The simple fact of diverging evolutionary lineages shows that the same species (“machine”) can be improved in different ways under the influence of different external factors.     

Species concepts and the recognition of ancestors

Whether or not ancestral species can be recognised depends on the species concept adopted. A “metaspecies”; is a species that completely lacks autapomorphies, and which might (or might not) be ancestral to other species. Such taxa have been identified among both living and fossil organisms. Under the most commonly‐used species concepts (biological, evolutionary, phenetic, phylogenetic, ecological, recognition and cohesion), “metaspecies”; can be assumed to be ancestral. Even if the known members of a metaspecies are not ancestral to anything, parsimony dictates that the (as yet unknown) ancestral lineage is identical to the metaspecies and, under these species concepts, assignable to the same species. Only the cladistic and monophyletic species concepts would deny “metaspecies”; ancestral status, but these species concepts are problematical and have never been used by practising systematists.     

Social is Emotional

This is a biological approach to the philosophy of mind that feeds an investigation of the phenomena of “social” and “emotional”, both of which are widespread in nature. I scrutinize the non-dualistic Darwinian concept of the continuity of mind. For practical reasons, I address mind at different levels of organization: The systemic mind are the properties of which a common, coherent evolution works upon. Separated from this is “language-mind”: the crystallization of thought in words, which is a strictly human phenomenon. As the phenomenology of the body is a theory of philosophy that lie beyond language it can—to a certain extent—be extrapolated across a species boundary. In the process the phenomenology of the body comes to resemble biosemiotics and with this tool, I investigate a field study of social play behavior in canids. This leads to a possibility to study the non-human experience of emotion as “locally meaningful phenomena”.     

Evolutionary theory and systematics: relationships between process and patterns

The relevance of the Modern Evolutionary Synthesis to the foundations of taxonomy (the construction of groups, both taxa and phyla) is reexamined. The nondimensional biological species concept, and not the multidimensional, taxonomic, species notion which is based on it, represents a culmination of an evolutionary understanding. It demonstrates how established evolutionary mechanisms acting on populations of sexually reproducing organisms provide the testable ontological basis of the species category. We question the ontology and epistemology of the phylogenetic or evolutionary species concept, and find it to be a fundamentally untenable one. We argue that at best, the phylogenetic species is a taxonomic species notion which is not a theoretical concept, and therefore should not serve as foundation for taxonomic theory in general, phylogenetics, and macroevolutionary reconstruction in particular. Although both evolutionary systematists and cladists are phylogeneticists, the reconstruction of the history of life is fundamentally different in these two approaches. We maintain that all method, including taxonomic ones, must fall out of well corroborated theory. In the case of taxonomic methodology the theoretical base must be evolutionary. The axiomatic assumptions that all phena, living and fossil, must be holophyletic taxa (species, and above), resulting from splitting events, and subsequently that evaluation of evolutionary change must be based on a taxic perspective codified by the Hennig ian taxonomic species notion, are not testable premises. We discuss the relationship between some biologically, and therefore taxonomically, significant patterns in nature, and the process dependence of these patterns. Process-free establishment of deductively tested “genealogies” is a contradiction in terms; it is impossible to “recover” phylogenetic patterns without the investment of causal and processual explanations of characters to establish well tested taxonomic properties of these (such as homologies, apomorphies, synapomorphies, or transformation series). Phylogenies of either characters or of taxa are historical-narrative explanations (H-N Es), based on both inductively formulated hypotheses and tested against objective, empirical evidence. We further discuss why construction of a “genealogy”, the alleged framework for “evolutionary reconstruction”, based on a taxic, cladistic outgroup comparison and a posteriori weighting of characters is circular. We define how the procedure called null-group comparison leads to the noncircular testing of the taxonomic properties of characters against which the group phylogenies must be tested. This is the only valid rooting procedure for either character or taxon evolution. While the Hennig -principle is obviously a sound deduction from the theory of descent, cladistic reconstruction of evolutionary history itself lacks a valid methodology for testing transformation hypotheses of both characters and species. We discuss why the paleontological method is part of comparative biology with a critical time dimension ana why we believe that an “ontogenetic method” is not valid. In our view, a merger of exclusive (causal and interactive, but best described as levels of organization) and inclusive (classificatory) hierarchies has not been accomplished by a taxic scheme of evolution advocated by some. Transformational change by its very nature is not classifiable in an inclusive hierarchy, and therefore no classification can fully reflect the causal and interactive chains of events constituting phylogeny, without ignoring and contradicting large areas of corroborated evolutionary theory. Attempts to equate progressive evolutionary change with taxic schemes by Haeckel were fundamentally flawed. His ideas found 19th century expression in a taxic perception of the evolutionary process (“phylogenesis”), a merger of typology, hierarchic and taxic notions of progress, all rooted in an ontogenetic view of phylogeny. The modern schemes of genealogical hierarchies, based on punctuation and a notion of “species” individuality, have yet to demonstrate that they hold promise beyond the Haeckel ian view of progressive evolution.     

Interspezifische Variabilität bei hypotrichen Ciliaten1

Interspecific variability in hypotrichous ciliates The genome organization of hypotrichous ciliates differs fundamentally from those of most other eukaryotic organisms. Every cell has two kinds of nuclei as is characteristic for ciliatese small generative micronuclei (Mi) whose DNA has a high molecular weight and which is organized in chromosomes, and vegetative macronuclei (Ma) which are very rich in DNA. The macronuclear DNA consists of so-called “gene-sized” DNA pieces, an organization which is not found in any other organism. This extraordinary genome organization offers a convenient experimental approach for studying evolutionary divergence at different molecular levels: 1. whole genomes, 2. subfractions of genomes, and 3. enzyme proteins. The comparison of unfractionated genomic DNA of hypotrichous ciliates by Dna-DNA hybridizations has yielded an unsuspected result: species that are closely related according to their morphology show an unusually low amount of sequence homology. The underlying reason might be that hypotrichous species separated early in eukaryotic evolution. Whereas the morphology of “closely related” species has changed only little, molecular evolution has led to major genomic changes that reflect the great evolutionary age of the species. The separation of native macronuclear DNA by gel electrophoresis produces species-specific DNA banding patterns based on different copy numbers of individual “gene-sized” DNA pieces in different species. These banding patterns allow the discrimination of sibling species which are morphologically very similar or even undistinguishable. Higher taxa can also be identified by means of DNA banding patterns. Cloned α- and β-tubulin genes were used in hybridization experiments to study the evolutionary divergence of individual DNA sequences in different hypotrichous species. The unusual Magenome organization makes such an analysis especially convenient. Characteristics of individual genes such as length number of sequence variants, copy number, and pattern of restriction sites can be compared with this method. The digestion of Mi-DNA with restriction endonucleases reveals differences in the repetitive DNA fraction of those genomes. Specific differences can be detected between closely related species and even between different populations of one species. The comparison of evolutionary divergence at the DNA level was supplemented by a comparison at the protein level. Enzyme electrophoresis proved to be a suitable method for the identification of otherwise indistinguishable species. Genetic ivergency (D-values) was estimated on the basis of allozyme data and a dendrogram was constructed reflecting the amount of genetic similarity between the species investigated. The discussion considers advantages and disadvantages of molecular characteristics for attacking taxonomic, phylogenetic, and evolutionary problems.     

Species: kinds of individuals or individuals of a kind

The “species‐as‐individuals” thesis takes species, or taxa, to be individuals. On grounds of spatiotemporal boundedness, any biological entity at any level of complexity subject to evolutionary processes is an individual. From evolutionary theory flows an ontology that does not countenance universal properties shared by evolving entities. If austere nominalism were applied to evolving entities, however, nature would be reduced to a mere flow of passing events, each one a blob in space–time and hence of passing interest only. Yet if there is genuine biodiversity in nature, if nature is genuinely carved into species, and taxa, then these evolutionary entities will be genuinely differentiated into specific kinds, each species being one of its kind. Given the fact that evolving entities have un‐sharp boundaries, an appropriately weak, “non‐essentialist” concept of natural kind has to be invoked that does not allow for strong identity conditions. The thesis of this paper is that species are not either individuals, or natural kinds. Instead, species are complex wholes (particulars, individuals) that instantiate a specific natural kind. © The Willi Hennig Society 2007.     

SHORT NOTES

Bock, W. 2000. Heuristics in systematics. Ostrich 71 (1 &; 2): 41–44.

Avian systematics is not only part of the science of ornithology, but serves heuristically as a foundation for many other analyses in ornithology. Systematics can be divided roughly into two major areas, namely species-level analyses and supraspecific classification. Of greatest significance is the distinction between provisional classifications and standard sequences, the latter are based on widely accepted classifications and have major useful functions such as the arrangement of taxa in handbooks, check-lists, and museum collections. The species concept is part of evolutionary theory, not systematics, and applies to contemporaneous groups of individual organisms. Clear distinctions separate the species concept, the species category, the species taxon, and the phyletic lineage—all usually designated as the “species”. The frequent practice of recognising all distinctive allopatric forms as separate species taxa results in two discrete classes of species taxa which largely destroys their usefulness for other biological analyses, including conservation efforts.     

Confocal-based cell-specific finite element modeling extended to study variable cell shapes and intracellular structures: The example of the adipocyte

This communication extends the recently reported cell-specific finite element (FE) method in Slomka and Gefen (2010) in which geometrically realistic FE cell models are created from confocal microscopy scans for large deformation analyses. The cell-specific FE method is extended here in the following aspects: (i) we demonstrate that cell-specific FE is versatile enough to deal with cells of substantially different geometrical shapes. The examples of an “elongated” pre-adipocyte and a “round” mature adipocyte are used to demonstrate this feature. (ii) We demonstrate that cell-specific FE can be used to analyze the mechanical behavior of cells that incorporate complex intracellular structures and are subjected to large deformations—again through the example of an adipocyte which contains a multitude of lipid droplets, each having a different size and shape. By demonstrating feasibility of inclusion of such inhomogeneities in the cytoplasm, the present work paves the way for modeling cellular organelles such as Golgi bodies, lysosomes and mitochondria in mechanically loaded cells using cell-specific FE.     

Problems of multi-species organisms: endosymbionts to holobionts

The organism is one of the fundamental concepts of biology and has been at the center of many discussions about biological individuality, yet what exactly it is can be confusing. The definition that we find generally useful is that an organism is a unit in which all the subunits have evolved to be highly cooperative, with very little conflict. We focus on how often organisms evolve from two or more formerly independent organisms. Two canonical transitions of this type—replicators clustered in cells and endosymbiotic organelles within host cells—demonstrate the reality of this kind of evolutionary transition and suggest conditions that can favor it. These conditions include co-transmission of the partners across generations and rules that strongly regulate and limit conflict, such as a fair meiosis. Recently, much attention has been given to associations of animals with microbes involved in their nutrition. These range from tight endosymbiotic associations like those between aphids and Buchnera bacteria, to the complex communities in animal intestines. Here, starting with a reflection about identity through time (which we call “Theseus’s fish”), we consider the distinctions between these kinds of animal–bacteria interactions and describe the criteria by which a few can be considered jointly organismal but most cannot.     

SPACES,BARRIERS, AND ION CARRIERS: ION ABSORPTION BY PLANTS

Epstein , Emanuel . (U. California, Davis.) Spaces, barriers, and ion carriers: ion absorption by plants. Amer. Jour. Bot. 47(5) : 393—399. 1960.—Ions from the external medium initially invade “outer” or “free” spaces of plant cells and tissues, by diffusion and ion exchange. This process is essentially non-metabolic and non-selective, and is readily reversible. The spaces accessible in this manner seem to be confined to the cell walls. From here, ions are selectively transported into “inner” spaces separated from the “outer” space by diffusion barriers. Ion carriers accomplish the selective transfer of the ions across the barriers or membranes, first into the cytoplasm and thence into the vacuole. The second step, into the vacuole, can be by-passed by those ions moving into the xylem elements and up to the shoot, and some transport to the shoot may skirt the active transport mechanisms entirely.     

Wohin steuert die Taxonomie?

In taxonomy, the organisms may be grouped into species according to different criteria, e.g. according to phenotypic and genetic characteristics or according to reproductive connections. In nature, there is no universal unit that can be called “species”, because different biological mechanisms are responsible for how individuals are grouped together or delimitated from each other. Different species concepts do not necessarily define the same entity existing in nature. One and the same individual can be assigned to different species depending on the species concept. In the last two decades, the barcode taxonomy has played a dominant role. A major advantage of the barcode taxonomy is the time‐saving automated mass detection of species without the need for taxonomically trained experts. Especially in evolutionarily young species, however, there are considerable discrepancies between the classification according to the barcode concept and the classification according to reproductive communities or phenotypic characteristics. The barcode species must therefore be understood as a species in addition to other species concepts.     

De-extinction and the conception of species

Developments in genetic engineering may soon allow biologists to clone organisms from extinct species. The process, dubbed “de-extinction,” has been publicized as a means to bring extinct species back to life. For theorists and philosophers of biology, the process also suggests a thought experiment for the ongoing “species problem”: given a species concept, would a clone be classified in the extinct species? Previous analyses have answered this question in the context of specific de-extinction technologies or particular species concepts. The thought experiment is given more comprehensive treatment here. Given the products of three de-extinction technologies, twenty-two species concepts are “tested” to see which are consistent with the idea that species may be resurrected. The ensuing discussion considers whether or not de-extinction is a conceptually coherent research program and, if so, whether or not its development may contribute to a resolution of the species problem. Ultimately, theorists must face a choice: they may revise their commitments to species concepts (if those concepts are inconsistent with de-extinction) or they may recognize de-extinction as a means to make progress in the species problem.