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microtubule-deficient macronuclei can divide as the somatic cortex appears to play a crucial role in positioning and even elongating the macronucleus (Jaeckel-Williams, 1978; Tucker et al., 1980). Microtubules and microfilaments are also implicated in micronuclear division , although the relative importance of each to chromosomal movement has not been resolved (LaFountain & Davidson, 1980; Lewis, Witkus, & Vernon, 1976). Spindle microtubules in the dividing micronucleus of Paramecium typically have 15 protofilaments compared to the \u201cnormal\u201d 13 for other organelles (Eichenlaub-Ritter & Tucker, 1984). The macronucleus in oligohymenophoreans , as for ciliates in general, varies in size, and therefore DNA amount, with cell size (e.g., Kazubski, 1963; Lynn & Berger, 1972, 1973; Morat, 1982). Division of the macronucleus is often slightly unequal (Berger, 2001; Morat, 1982). Yet, ciliates maintain a roughly proportional nuclear:cytoplasmic ratio over the course of many cell cycles. The mecha- nisms responsible for this regulation have been extensively explored, especially in Paramecium (Berger, 2001). Nilsson (2000) has argued that the minimal units of segregation during macronuclear division in Tetrahymena represent full genomes, although how this is accomplished remains to be explained. The macronucleus in oligohymenophoreans develops from a product of the zygotic nucleus , which typically divides two or three times to pro- vide nuclei for differentiation (Raikov, 1972). The macronuclear anlage undergoes a series of changes in its fine structure until it has developed nucleoli and begins transcription (Weiske-Benner & Eckert, 1985). As in the spirotrichs ( see Chapter 7 ), the development of the oligohymenophorean anlage involves DNA amplification , chromosome frag- mentation , sequence elimination , addition of telom- eres , and amplification of some genes, particularly ribosomal genes (Prescott, 1994; Schmidt, 1996). Moreover, this development may be epigenetically regulated by the parental or maternal macronu- cleus, even to the level of the precise excision of eliminated sequences (Meyer & Duharcourt, 1996; Preer, 2000). Much of the research on oligohymenophoreans has focused on Paramecium and Tetrahymena in which chromosome fragmentation and sequence elimination occur by different mechanisms. In Paramecium , a terminal inverted repeat unit flanks the internally eliminated sequences (IESs) and bears some similarity to the transposable elements found in spirotrichs (Klobutcher & Herrick, 1995, 1997). The quality of this flanking sequence is critical as single base pair changes in it can prevent IES elimination (Mayer, Mikami, & Forney, 1998; Matsuda, Mayer, & Forney, 2004). In Tetrahymena , a consensus sequence has not been identified, appar- ently leading to less precision in the elimination of sequences (Austerberry, Snyder, & Yao, 1989; Yao, Duharcourt, & Chalker, 2002). However, there is an internal 10-bp core to the chromosome breakage sequence \u2013 AAACCAACC?C \u2013 that is completely conserved and possibly represents a regulatory protein binding site (Hamilton et al., 2006). Sequence\u2212specific information may also be provided by molecules, for example by small RNAs, that derive from the parental macronucleus and that can control DNA rearrangements and processing in the developing macronucleus through homology- dependent mechanisms (Kowalczyk, Anderson, Arce-Larreta, & Chalker, 2006; Le Mouel, Butler, Caron, & Meyer, 2003; Meyer, Butler, Dubrana, Duharcourt, & Caron, 1997). In both cases, the processes of fragmentation of and excision from micronuclear chromosomes result in macronuclear \u201cchromosomes\u201d that are shorter than the micronuclear chromosomes, although not as short as the gene-sized pieces of spirotrichs ( see Chapter 7 ). Oligohymenophorean macronuclear chromosomes range in size from from 20\u20132,500 kb for Paramecium species (Rautian & Potekhin, 2002; Steele, Barkovy- Gallagher, Preer, & Preer, 1994), from 21\u20131,500 kb in Tetrahymena (Altschuler & Yao, 1985; Conover & Brunk, 1986), and from 2\u2013300 kb in Glaucoma (Katzen, Cann, & Blackburn, 1981). Breakage of micronuclear chromosomes forms many new chro- mosome \u201cends\u201d, and this has provided ciliate molecu- lar biologists with a useful model to investigate the structure, formation, and maintenance of telomeres (Blackburn, 1986). The CCCCAA oligonucleotide repeat characterizes the telomeres of the macronu- clear chromosomes of Tetrahymena (Blackburn & Gall, 1978; Yao & Yao, 1981), Glaucoma (Katzen et al., 1981), and Paramecium (Yao & Yao, 1981). The abundance of ends and the need for their re-construc- tion and maintenance lead to the discovery of the ribonucleoprotein enzyme complex responsible for these processes, now called telomerase (Blackburn, 1992; Greider & Blackburn, 1987). Some years prior to these discoveries, it had been possible to separate micronuclei and macro- nuclei, so that at least pure macronuclear prepara- tions could be analyzed for sequence complexity (Gorovsky, Yao, Keevert, & Pleger, 1975; Soldo & Godoy, 1972). With renaturation kinetic analyses, 15.6 Nuclei, Sexuality and Life Cycle 321 322 15. Subphylum 2. INTRAMACRONUCLEATA: Class 9. OLIGOHYMENOPHOREA most macronuclear DNA sequences behaved as unique sequences, with very little highly repeated sequences and up to 20% moderately repetitive (McTavish & Sommerville, 1980; Soldo & Godoy; Yao & Gorovsky, 1974). The highly and moder- ately repetitive fraction are apparently eliminated during development of the macronuclear anlage (Yao & Gall, 1979). As for other classes of ciliates, examples are now accumulating of genetic code deviations among oligohymenophoreans . Of the three universal stop codons \u2013 UAA, UGA, and UAG, oligohymeno- phoreans , such as the hymenostome Tetrahymena (Horowitz & Gorovsky, 1985), the peniculine Paramecium (Caron & Meyer, 1985; Preer, Preer, Rudman, & Barnett, 1985), and the peritrichs Vorticella and Opisthonecta (Sánchez-Silva et al., 2003) use only UGA. The codons UAA and UAG are now used by Paramecium and Tetrahymena as sense codons for glutamine and glutamic acid (Caron & Meyer; Preer et al., 1985), while UAA has been confirmed as the \u201cglut\u201d codon in peri- trichs (Sánchez-Silva et al., 2003). There are two explanations for these deviations. First, tRNAs have been described that decode for these novel amino acid assignments (Hanyu, Kuchino, & Nishimura, 1986; Sánchez-Silva et al., 2003). As with genetic code deviations in other ciliates, another explana- tion is the evolution of translational release factors with a higher specificity for one or other of the universal stop codons (Caron, 1990). This predic- tion was confirmed by analyses of the spirotrich eukaryotic release factor 1, which is the protein that recognizes stop codons and terminates transla- tion (Inagaki & Doolittle, 2001; Lozupone, Knight, & Landweber, 2001). This higher specificity then allowed the evolution of tRNA anticodons to use the now-available and unused stop codons. Conjugation of oligohymenophoreans , typed as temporary and equal or isogamontic in most groups, was first described by Hertwig (1889) in Paramecium (Raikov, 1972). However, the peri- trichs conjugate by total cell fusion, typically of unequal-sized conjugants ; they are therefore ani- sogamontic (Raikov, 1972). The macroconjugant is large and sessile while the microconjugant is small and free-swimming. Microconjugants may arise by unequal cell division, rapid successive divisions without intervening growth or direct transforma- tion of microzooids in Zoothamnium species that show colonial polymorphism (Raikov, 1972). The endosymbiotic apostome Collinia , described by Collin (1909a) as an Anoplophrya species, appears to undertake