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The origin of eukaryotic cells is a mystery second only to the origin of life itself. The problem is that eukaryotes make up a distinctive clade, conspicuously different from prokaryotes, yet they share genes and traits with both Bacteria and Archaea. There is general agreement that eukaryotes are chimaeric, since mitochondria and plastids derive from Bacterial endosymbionts; but consensus ends here. Disputes swirl around the nature of the cells that hosted those symbionts, the nature and timing of their association, and the role of the symbionts in generating eukaryotic complexity. This long-running controversy may now be approaching a resolution that combines ideas from several camps. The emerging synthesis postulates an “urkaryote” of Archaeal affinities that diverged very early and came to make its living by scavenging and predation upon the primary producers of organic matter. Acquisition of the Bacterial precursors of mitochondria enhanced the consortium's energy economy, and underwrote the rise of complex eukaryotic cells.

This chapter introduces the structures and processes of the eukaryotes, the branch of life that includes all plants and animals. It discusses eukaryotic gene structure and transcription, components of the eukaryotic cell, and lifestyles of the single-celled eukaryote.

This chapter introduces some of the concepts central to Génti's main argument, and illustrates how the core problem of the nature of the living state applies at many levels of life. Topics discussed include the chemoton, life at the prokaryotic level, life at the animal level, and eukaryotic cells and fungi.

A series of major transitions in evolution has generated the biological hierarchy (e.g., genes in cells, cells in organisms, organisms in societies) observed today. Each transition requires that previously selfish, free-living individuals join together to form a group resembling an individual in its own right. This book seeks to identify the principles of social evolution that underlie the major transitions, focusing on the evolution of the eukaryotic cell, sexual reproduction, multicellularity, eusociality, and interspecific mutualisms. It suggests that each major transition has three stages – social group formation, social group maintenance, and social group transformation. Using Hamilton's inclusive fitness theory (kin selection theory) as its conceptual foundation, the book investigates two underexplored issues. First, to what extent do common principles operate at each stage of the major transitions and what is the evidence for their operation; and second, what are the principles underlying social group transformation?

Pathways of social group formation are poorly known for the origin of the eukaryotic cell, sexual reproduction, and many interspecific mutualisms. In the origin of multicellularity and eusociality, social group formation has usually occurred via a subsocial pathway (association of parents and offspring), with a semisocial pathway (association of same-generation organisms) occurring occasionally. The essential genetic condition for social group formation in groups exhibiting altruism is that relatedness should be positive – a prediction overwhelmingly supported by available evidence in the case of both the origin of multicellularity and the origin of eusociality. Non-genetic factors (ecological or synergistic) facilitate social group formation by increasing the benefits of grouping and the costs of living singly. Ecological factors promoting the formation of multicellular organisms and eusocial societies include environmental stresses and predator pressure. A major synergistic factor promoting the formation of multicellular organisms, eusocial societies, and interspecific mutualisms is division of labour.

If a product is synthesized intracellularly and not secreted by the producing cell, or if the product is to be extracted from plant, animal, or fungal tissue, it is necessary to remove the product from the cell or tissue by force. The choice of procedure is highly dependent on the nature of the product and the nature of the cell or tissue. It was seen in Chapter 1 that bioproducts represent a wide variety of chemical species. In this chapter, we also see that the sources of bioproducts—cells and tissues—are widely varied. For this reason, there exists a wide variety of methods for breaking, or lysing, cells and tissues, broadly classified as “chemical” and “physical” methods. Once cells have been suspended and/or broken open, the resulting suspension of solids must be separated from the liquid in which it is suspended. This separation process, filtration and/or sedimentation (the subjects of the next two chapters), is enhanced by having larger particles. Larger particles can be achieved by flocculation, a process whereby particles are aggregated into clusters, or flocs. In recent years, it has become desirable to isolate specific cell types from mixtures of suspended cells and to deliver the resulting cell subpopulation(s) to a process for which they, and only they, are required. Most examples come from in vivo sources such as blood and dispersed tissue cells. This aspect of cell processing, namely, cell purification, places special demands on separation processes that are capable of handling particulate matter under conditions that allow cells to remain alive. This chapter presents two major elements of cell processing: the science and engineering of cell rupture by physical and chemical methods and the flocculation of cells and subcellular particles in aqueous suspension. First, however, it is helpful to develop a broad appreciation for the variety and compositions of cells that are likely to be encountered in downstream bioprocessing.

This chapter presents exciting new evidence for and an interpretation of life’s deepest, most potentially profound level of chimerical union. It shows that genetic and molecular biological evidence supports the notion of the oldest organisms that merged in the formation of the modern nucleated (eukaryotic) cell, and arguably the most important for intracellular motility, was, and still is, the remnant spirochete. This chapter shows that kinetosomes, centrioles, and centrosomes display tantalizing evidence of a common origin. It hypothesizes that the undulipodium evolved from a common spirochete ancestor.

This chapter explains how bacterial genophore evolved into animal (including human) chromosomes. It reviews the transition from the bacterial carrier of DNA to the chromosomes within the more complex eukaryotic cells. This chapter shows that mechanical tension among continuously attached chromosomes is the essential signal for the sets of chromosomes to move in a coordinated way as “mitotic plates.” It suggests that the physicochemical basis for the inheritance of the human sensory system is coded in the DNA of the genome.

Centromeres and the kinetochore proteins that bind them are required for chromosome segregation during eukaryotic cell division. Despite this conserved function, both centromeric DNA and kinetochore proteins evolve rapidly. This chapter hypothesizes that this paradox can be explained by an on-going conflict between selfish centromeric DNA elements and the DNA binding proteins of the kinetochore. In this model, centromeres are able to gain an evolutionary advantage by promoting their own transmission during asymmetric female meiosis. Deleterious consequences of this selfish behaviour in turn select for variant kinetochore proteins that can suppress centromeric imbalances. This conflict, termed ‘Centromere Drive’, provides an explanation for observed differences in evolutionary rates between components of the kinetochore, and makes predictions about which taxa might experience accelerated centromeric evolution.

The widespread practices of viniculture (the study of production of grapes for wine) and oenology (the study of winemaking) affirm the generalization that grapevines have fewer problems with mineral deficiency than many other crops. Only occasionally is the addition of iron (Fe), phosphorus (P), magnesium (Mg), and manganese (Mn) supplements to the soil needed. Addition of potassium (K), zinc (Zn), and boron (B) to the soil is more common. And, of course, nitrogen (N) is critical for the production of proteins. Over the years, various transition metals (metals in groups three through twelve [3–12] of the periodic table, Appendix 1) have been shown to be generally important. These groups include iron (Fe), magnesium (Mg), manganese (Mn), zinc (Zn), and copper (Cu). Many metals are bound to organic molecules that are important for life. Some of the metals, such as copper (Cu) and iron (Fe), are important in electron transport while others, including manganese (Mn) and iron (Fe), inhibit reactive oxygen (O) species (ROSs) that can destroy cells. Metals serve both to cause some reactions to speed up, called positive catalysis while causing others (e.g., unwanted oxidation) to slow down (negative catalysis). It is not uncommon to add nitrogen (N), in the form of ammonium salts such as ammonium nitrate (NH₄NO₃), as fertilizer to the soil in which the vines are growing. It is also common to increase the nitrogen (N) content in the soil by planting legumes (legumes have roots that are frequently colonized by nitrogen-fixing bacteria). Nitrogen- fixing bacteria convert atmospheric nitrogen (N₂), which plants cannot use, to forms, such as ammonia (NH₃) or its equivalent, capable of absorption by plants. Nitrogen, used in plant proteins, tends to remain in the soil after harvest or decomposition. With sufficient nitrogen present in the soil the growth cycle can begin again in the following season without adding too much fertilizer. In a more general sense, however, it is clear (as mentioned earlier) that the soil must be capable of good drainage so the sub-soil parts of the plant do not rot and it must be loose enough to permit oxygen to be available to the growing roots.