Recurrent Motifs Research Articles

Complex Systems: From chemistry to systems biology

There is great interest in complex systems in chemistry, biology, engineering, physics, and gene networks, among others. The complexity comes from the fact that in many systems there are a large number of variables, many connections among the variables including feedback loops, and many, usually nonlinear, equations of motion, or kinetic and transport equations. “Many” is a relative term; a properly interacting system of just three variables can show deterministic chaos, a complex behavior indeed. For the natural scientist and the engineer, nearly all their systems are complex. Many problems still resist the arguments of symmetry, averaging, timescale separation, and covariation that often underlie complexity reductions. New tools have allowed us to peer at even the nanometer scale of the structure of materials, explore the dynamic chemical composition of the explosions in our increasingly efficient engines, and determine the organization of the genome and architecture of the molecules and molecular networks it implicitly encodes. All these are revealing extraordinary arrangements of kinetic processes, feedback loops, and spatial organization that together create complex behaviors. The recent interest is due, in part, to the substantial advances in measurement techniques of chemical and biological species and experiments on complex systems, concurrent substantial advances in theory, and the increased urgency of analyzing and understanding complex systems of fundamental importance. Nowhere is the importance of complex dynamics and architectures clearer than in biological systems. In this issue, all of the articles address problems of complexity in organisms. Topics range from information processing in their signaling network and the organization of their metabolism, to how populations of differentiated cells communicate with one another to coordinate behavior, and to how evolution has arrived at different recurrent motifs … 1To whom correspondence should be addressed. E-mail: john.ross{at}stanford.edu

Frequency and isostericity of RNA base pairs

Most of the hairpin, internal and junction loops that appear single-stranded in standard RNA secondary structures form recurrent 3D motifs, where non-Watson–Crick base pairs play a central role. Non-Watson–Crick base pairs also play crucial roles in tertiary contacts in structured RNA molecules. We previously classified RNA base pairs geometrically so as to group together those base pairs that are structurally similar (isosteric) and therefore able to substitute for each other by mutation without disrupting the 3D structure. Here, we introduce a quantitative measure of base pair isostericity, the IsoDiscrepancy Index (IDI), to more accurately determine which base pair substitutions can potentially occur in conserved motifs. We extract and classify base pairs from a reduced-redundancy set of RNA 3D structures from the Protein Data Bank (PDB) and calculate centroids (exemplars) for each base combination and geometric base pair type (family). We use the exemplars and IDI values to update our online Basepair Catalog and the Isostericity Matrices (IM) for each base pair family. From the database of base pairs observed in 3D structures we derive base pair occurrence frequencies for each of the 12 geometric base pair families. In order to improve the statistics from the 3D structures, we also derive base pair occurrence frequencies from rRNA sequence alignments.

Dorothy M. Richardson’s “The Garden” as an Amplification of a Recurrent Epiphanic Moment in Pilgrimage

This paper analyses Dorothy Richardson’s short story “The Garden” (1924) as an amplification of the recurring epiphanic garden scenes in Pilgrimage. “The Garden” could be considered a close-up of the episode recreated in the Pilgrimage garden memories seen through the eyes of a small child. In this short story there are no epiphanic implications, only the ordinary perceptions of a small child on a common day. However, when the protagonist of Pilgrimage remembers the childhood episode when she contemplated the flowers in the garden by herself, it is so full of significance and poetry that it becomes a symbol, a recurrent epiphanic motif that is a source of meaning and peace

Theatrical Nationalism: Exposing the “Obscene Superego” of the System

Nationalism has been an important facet of theatrical expression since the Greeks. The earliest extant Greek play, The Persians by Aeschylus, reveals the ingenious tactics of the Greeks in defeating the Persians in the battle of Salamis, and much of Greek tragedy emphasizes the superiority of the Athenian city-state to other polities. Cultural nationalism flourished particularly in the nineteenth century, following the American and French revolutions, the partition of Poland, and the Napoleonic invasion of much of Europe. Nationalist movements developed in the many nations of Europe, in some cases calling for independence from a foreign oppressor. Theatre was recognized as a useful means for formulating and solidifying notions of national identity. National theatres, especially in countries that were not yet nation-states, were established to further the aims of nationalists. In the twentyfirst century, national theatres continue to play an important role in conserving national cultures, especially in Europe, and cultural nationalism remains a recurrent motif. I will discuss some of the earlier features of nationalism in the theatre and show how they have been retained in theatrical expression today, especially in the National Theatre of Scotland. I will also demonstrate how certain theatre artists, such as Christoph Schlingensief in Austria and Janez Jansa in Slovenia, who employ a mode of “subversive affirmation,” have turned the tables on cultural nationalism at local, national, and transnational levels, ironizing it and rendering it obscene. According to Inke Arns and Sylvia Sasse,

Dances of the Self in Heinrich von Kleist, E. T. A. Hoffmann and Heinrich Heine (review)

Reviewed by: Dances of the Self in Heinrich von Kleist, E. T. A. Hoffmann and Heinrich Heine Jeffrey L. Sammons Lucia Ruprecht, Dances of the Self in Heinrich von Kleist, E. T. A. Hoffmann and Heinrich Heine. Aldershot, England, and Burlington, Vermont: Ashgate, 2006. xvi + 158 pp. In regard to the art of the dance, the default position, so to speak, for this study is the classical ballet that dominated the stage in the nineteenth century. It is the bodily movement counterpart to the Winckelmannian sculptural ideal, striving for vertical elevation, causing the body to disappear, and concealing bodily pain as alleged of the Laocoön sculpture. It requires the disciplining of subjectivity and spontaneity. It therefore can be understood as conservative and repressive, so that subversive writers, such as Kleist, Hoffmann, and Heine, regard it with hostility and imagine alternative modes of dance. In Kleist’s essay on the marionette theater, classical ballet teaching produces failure. As against the vertical tendency of ballet, “[s]oul takes shape in a curved line” (33); Kleist appears to be revising or at least reversing Schiller’s opposition of grace with self-consciousness and defines a tension between weight and weightlessness. Bodily movement is performance, oscillating “between the wish for authenticity and the need for posing” (35). Ruprecht comments on the feminization of the male dancer, noting that when the youth imitating the thorn-drawer loses his gracefulness, he recovers his gender as a man, though a failed one. Ruprecht pursues the recurrent motif of falling throughout Kleist’s works, from which rising is a kind of relative survival. If the Marionettentheater permits a reasonably optimistic reading, Hoffmann’s vision is much darker. Hoffmann disliked ballet and its music; he did not include a ballet in his opera Undine. He prefers “a synthesis of movement, mime and meaning” (63) and the carnivalistic randomness of the commedia dell’arte to the disciplined repetitiousness of the classical mode. Repetitiousness is thematic in Der Sandmann, in the regularity and flawlessness of the automaton Olimpia and in Nathanael’s “re-enactments of the traumatic primal scene” (67). Nathanael lacks the self-knowledge to escape the traumatic repetition, while the narrator is saved by the irony that his character lacks. The fantastic choreography of Prinzessin Brambilla is liberating, countering repetition with creative theatricality and metamorphosis. Yet the dancers frighten themselves also; “their delight in role-play is but the reverse of a pathological surrender to a schizophrenic sense of self” and “[t]he dancing Giglio becomes a mirror of the reader who tries to get hold of the text” (93). Nevertheless, “dialogic dances engender stability through motion, a form of stability that the paralysed Nathanael lacks” (95). As has long been noted, dance motifs are significant in Heine’s writing. Ruprecht concentrates most of her attention on the dancing of Mademoiselle [End Page 270] Laurence in Florentinische Nächte, which does not achieve classical purity and wholeness; its deformation of classical myth mirrors the modern mind, transgresses conventions, and prefigures forms of modern dance. In the course of the discussion Ruprecht undertakes something that has never been done before: she moves from her discussion of Heine to an analysis of the ballet Giselle, the scenario of which Gautier took from Heine’s Elementargeister. The result is what one would expect; the ballet conventions oblige Giselle’s movement to be confined, while Laurence’s dance “breaks with the code of movement set by classical ballet technique” (114) and leads to a new aesthetic. I have here confessedly attempted to abstract the sort of interpretive points that interest me most from a dense and abstruse cultural-studies discourse that roams from Freud to, among others, Derrida, Foucault, Lacan, and Judith Butler; thus I have doubtless truncated the aspect of the study that may be of most interest to others. Still, the broad synchronic range of cultural studies can foreshorten interpretation. This seems to me particularly the case with Heine; for all the acuteness of the close reading of Laurence’s performance, it does not comprehend the full significance of dance for him. Ruprecht begins the section with the bacchanalian ball in the Briefe aus Berlin, remarking of it that “it...

Fantasy Motif Metaphors: Magical Powers as Exceptionality in Disney’s The Incredibles and Zizou Corder’s Lion Boy trilogy


 
 
 While works of the fantasy genre convey literal stories which make sense according to the laws of their fictional worlds, the very impossibilities of these narratives invite further readings of their ‘secondary or tertiary levels of meaning’ (Bleiler 1983, p.vii; also see McGillis 1996a, p.72; Walsh 1981, p.38). Such readings have been generated through the analytical lenses of allegory, parable, fable, symbol and metaphor. A specific focus upon the operation of metaphor in recurrent fantasy motifs enables a precise analysis of fantasy’s secondary levels of meaning. Such a methodology scrutinises fantasy’s engagement with cultural assumptions and ideas, highlighting the ideological implications of fantasy and thus verifying fantasy’s inherent relevance to reality. This article aims to illustrate the value of this methodology by analysing the motif of magical powers as exceptionality in Disney’s The Incredibles (2003) and Zizou Corder’s Lion Boy trilogy (2003-2005).
 
 

The UA_handle: a versatile submotif in stable RNA architectures†

Stable RNAs are modular and hierarchical 3D architectures taking advantage of recurrent structural motifs to form extensive non-covalent tertiary interactions. Sequence and atomic structure analysis has revealed a novel submotif involving a minimal set of five nucleotides, termed the UA_handle motif (5′XU/ANnX3′). It consists of a U:A Watson–Crick: Hoogsteen trans base pair stacked over a classic Watson–Crick base pair, and a bulge of one or more nucleotides that can act as a handle for making different types of long-range interactions. This motif is one of the most versatile building blocks identified in stable RNAs. It enters into the composition of numerous recurrent motifs of greater structural complexity such as the T-loop, the 11-nt receptor, the UAA/GAN and the G-ribo motifs. Several structural principles pertaining to RNA motifs are derived from our analysis. A limited set of basic submotifs can account for the formation of most structural motifs uncovered in ribosomal and stable RNAs. Structural motifs can act as structural scaffoldings and be functionally and topologically equivalent despite sequence and structural differences. The sequence network resulting from the structural relationships shared by these RNA motifs can be used as a proto-language for assisting prediction and rational design of RNA tertiary structures.

The View from Castle Rock , and: Mothers and Sons (review)

Reviewed by: The View from Castle Rock, and: Mothers and Sons Judith Grossman (bio) Alice Munro, The View from Castle Rock (Alfred A. Knopf, 2006), 349 pp. Colm Tóibín, Mothers and Sons (Scribner, 2007), 270 pp. Alice Munro’s thirteenth book, The View from Castle Rock, carries an implicit message of valediction, preoccupied as it is with the writer’s origins and her mortality. While insisting in the Foreword that these are “stories,” Munro also concedes a few lines earlier that she has turned towards a personal past, “doing something closer to what a memoir does—exploring a life, my own life.” Part One of the book recalls, with characteristic indirection, her family’s history rather than her own (mainly through the Laidlaw paternal line), following hardscrabble shepherds, poor cousins of the Scottish writer James Hogg, through the ordeals of emigration to become farmers in the Canadian wilderness; and it ends with passages from her own father’s written recollection of those immigrants in old age. Yet it’s wholly consistent with Munro’s method of work that to explore any life means entering a complex narrative, branching out through time and through social and geographic space until we confront the mystery of self as both singular and plural, moment and location. “No Advantages,” the subtitle of this first section, derives from an early nineteenth-century account of the Ettrick Valley, home of the Laidlaw shepherds (Wordsworth’s famous elegy for James Hogg describes the place as “a bare and open valley,” although he goes on to embellish the scene with “golden leaves upon the pathways”). The dismissive phrase might also apply to the context of Alice Munro’s own childhood in Wingham, Ontario, to which she returns in Part Two. Her parents’ respectable poverty deepened with the collapse of a fox-farming enterprise and with the onset of her mother’s crippling illness, which threw the burden of housekeeping on Munro as the eldest daughter. “I waxed the worn linoleum. I ironed the worn dishtowels as well as the shirts and blouses, I scoured the battered pots and pans and took steel wool to the blackened metal shelves behind the stove.” The story of her escape to university as a scholarship student, against the odds, became a recurrent motif in her fiction—inseparable from the quickly made first marriage that would lock [End Page 649] the door against going back. For Munro knew, as all working-class girls of her era did, that she would be expected to return home until she got married. No wonder that a fear of domestic imprisonment haunts many young women in her stories. Hence too the quality of desperation in the announcement of Munro’s engagement here—“I meant to hang on to him”—along with her willed determination to love her fiancé, just as he was bent on rescuing her. The drama of this enormous leap in the dark is definitively rendered in “The Beggar Maid,” although Munro developed fresh variations in “Family Furnishings” and the superb late story “Post and Beam.” In each version the husband is given a different name—Patrick, or Brendan—and in the final, bleak and penitent rendering here, Michael (Wikipedia gives it as James): “He deserved better than me, Michael did. He deserved a whole heart.” But a whole heart would be precisely what Munro’s young women couldn’t have, given the divided loyalties that come with upward mobility. Leaving home (when a home has been all your endowment) is enough of a betrayal without remaking yourself in the image of another’s desire. In other ways, too, The View from Castle Rock becomes a revelatory sourcebook for Munro’s fiction. “The Wilds of Morris Township,” quoting verbatim from a great-uncle’s memoir, shows how that document was mined for Munro’s indelible story, “A Wilderness Station.” Notably, while the published records and memoirs were kept in this family by men, it’s the briefly named, hard-laboring women that Munro’s work pulls into the foreground. There is a passion for justice at work in “A Wilderness Station.” On the other hand, the writer’s grasp of her world’s severities...

Scenes of Translation: Responses to Responses

In his “Response to Responses,” Vicente Rafael thanks and answers the questions raised during the forum. To Gary Devilles’s comment of his “remaining silent” in the way translation can be “radicalized into an ethical technology or a strategic pedagogy,” Rafael offers the trope of revenge—a desire for justice, which results from the Spanish misrecognition of Filipino attempts at translation—and the language of secrecy and solidarity of the 1896 Revolution—which results from the failure of Castilian to become lingua franca—as political technics in themselves. To Ramon Guillermo’s comment of the book’s impoverished, restrictive, and imprecise notions of translation, Rafael reiterates and contends his multivalent conception of translation: always doubled and open-ended; dialectical and dialogical; “that which is new and for this reason yet to be assimilated and understood;” in sum, “that which is always inside and outside, eccentric yet inherent to the social order,” constitutive as well as disruptive. To Remmon Barbaza’s Heideggerian reading, Rafael thankfully re-emphasizes the recurrent motif of the foreign as call and the affinity of this with the foreign as promise. Finally, to Roland Tolentino’s “disconcerting” series of questions, Vince Rafael warns against the fetishization of translation when detached from its particularity, and its envisagement as “the subjugation of the other in order to realize one’s sense of self, a self predicated on the mastery of the other’s discourse.”

<em>Ars Moriendi</em>, the Erotic Self and AIDS

<em>Ars Moriendi</em>, the Erotic Self and AIDS

Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments

As modeling of changes in backbone conformation still lacks a computationally efficient solution, we developed a discretisation of the conformational states accessible to the protein backbone similar to the successful rotamer approach in side chains. The BriX fragment database, consisting of fragments from 4 to 14 residues long, was realized through identification of recurrent backbone fragments from a non-redundant set of high-resolution protein structures. BriX contains an alphabet of more than 1,000 frequently observed conformations per peptide length for 6 different variation levels. Analysis of the performance of BriX revealed an average structural coverage of protein structures of more than 99% within a root mean square distance (RMSD) of 1 Angstrom. Globally, we are able to reconstruct protein structures with an average accuracy of 0.48 Angstrom RMSD. As expected, regular structures are well covered, but, interestingly, many loop regions that appear irregular at first glance are also found to form a recurrent structural motif, albeit with lower frequency of occurrence than regular secondary structures. Larger loop regions could be completely reconstructed from smaller recurrent elements, between 4 and 8 residues long. Finally, we observed that a significant amount of short sequences tend to display strong structural ambiguity between alpha helix and extended conformations. When the sequence length increases, this so-called sequence plasticity is no longer observed, illustrating the context dependency of polypeptide structures.

The observed and energetically feasible crystal structures of 5-substituted uracils

A search of the Cambridge Structural Database for crystal structures of 5-substituted uracils shows that, although there is a recurrent motif with symmetric hydrogen bonding and interdigitation of the 5-substituent R, a range of other hydrogen bonded ribbons, sheets and three-dimensional motifs are possible. In order to try and rationalize this, we have performed a combination of experimental studies and computational searches for low energy structures for the 12 simple 5-substituted uracils with R = H, CH3, CH2CH3, CHCH2, CN, OH, NH2, NO2, F, Cl, Br and I. Crystallization experiments on these compounds yielded the first single crystal X-ray determinations of 5-ethyluracil and 5-cyanouracil, as well as low temperature redeterminations of the disordered structures of 5-chlorouracil and 5-bromouracil. The lattice energies were calculated for the known crystal structures and compared with the computed lattice energy landscape for each molecule (except R = Br and I). Although the symmetric ribbon motif often dominates the computed crystal energy landscape, all of the molecules show a variety of different hydrogen bonding structures within a small energy range (5 kJ mol−1) of the global minimum and exhibit quite a diverse range of energetically competitive motifs. Thus, the range of crystallization outcomes, from polymorphism and other multiple forms, to the difficulty in growing single crystals (R = CHCH2 and NH2) probably reflects the sensitivity of the various hydrogen bonding motifs to the substituent and limited range of crystallization conditions that can be applied.

Dinuclear Cp* Cobalt Complexes of the 1,2,4,5-Benzenetetrathiolate Bischelating Ligand

The dinuclear Cp*Co dithiolene complex [Cp*Co(btt)CoCp*] ( 1) is prepared in high yield from the reaction of the bis(dibutyltin) complex of 1,2,4,5-benzenetetrathiolate (btt) with 2 equiv of [Cp*Co(CO)I 2]. Mononuclear complexes are also obtained from 1,2,4,5-tetrakis(isopropylthio)benzene ( 2) and sodium in pyridine, from benzo[1,2- d;4,5- d ']bis(1,3-dithiolane-2,6-dione) ( 3) and ( t )BuOK in tetrahydrofuran, or from benzo[ d]-1,3-dithiolane-2-one ( 7) and ( t )BuOK to afford respectively 4a, 4b, and [Cp*Co(bdt)] ( 6), while [Cp*Co(dmit)] ( 8) is obtained by literature methods. The X-ray structures of the dinuclear complex 1 and the mononuclear complexes 4a and 6 were determined. They are all characterized by Cp* . . . btt face-to-face intermolecular interactions, leading to a recurrent 4-fold symmetry motif. The cyclic voltammograms of the [Cp*Co(dithiolene)] complexes performed in CH 2Cl 2 show reversible Co (III) to Co (II) reduction but irreversible oxidation waves. The large potential difference between the two reduction waves of the bimetallic complex 1 (269 mV) indicates a stable mixed-valence Co (III)-Co (II) state for the reduced [Cp*Co(btt)CoCp*] (-) anion. Upon trimethyl phosphite addition, the mono-P(OMe) 3 adduct [ 1.P(OMe) 3] exhibits a red shift of the low-energy absorption band to the IR region (856 nm, = 13 000 M (-1).cm (-1)), while [ 8.P(OMe) 3] exhibits a 150 nm blue shift. The stability constants of these P(OMe) 3 adducts were determined from UV-vis spectroscopic titration experiments, with, for example, log( K/mol (-1).dm (3)) values of 3.1 and 0.52 for the mono- and bis-adduct of 1, respectively. The electrochemical investigation of 1 and 8 in excess phosphite shows a strong current enhancement upon oxidation, attributable to the catalytic generation of the radical cation P(OMe) 3 (*+).

Recurrent design patterns in the feedback regulation of the mammalian signalling network

Biochemical networks are characterized by recurrent patterns and motifs, but the design principles underlying the dynamics of the mammalian intracellular signalling network remain unclear. We systematically analysed decay rates of 134 signalling proteins and investigated their gene expression profiles in response to stimulation to get insights into transcriptional feedback regulation. We found a clear separation of the signalling pathways into flexible and static parts: for each pathway a subgroup of unstable signal inhibitors is transcriptionally induced upon stimulation, while the other constitutively expressed signalling proteins are long-lived. Kinetic modelling suggests that this design principle allows for swift feedback regulation and establishes latency phases after signalling, and that it might be an optimal design due to a trade-off between energy efficiency and flexibility.

Sociomics: CESAGen Multidisciplinary Workshop on the Transformation of Knowledge Production in the Biosciences, and its Consequences 23–24 July, 2007 Wellcome Trust Genome Campus, Hinxton, UK

On 23 and 24 July, 2007, the Centre for Economic and Social Aspects of Genomics (CESAGen) held its first sociomics workshop at the Wellcome Trust Genome Campus, Hinxton, UK. The topic was transformation of knowledge production. Participants included social scientists together with those working on different elements of the proteomics knowledge production-line, including core facilities, data repositories, large-scale projects, MS, search engines, reference databases, standardisation and public funding. Recurrent motifs included gear-heads, black boxes, uncertainty and getting back to biology.

Beyond the Apocalypse: Czech Verse on the End of the Second World War

WHEN, today, one reads Czech verse concerned with the Second World War and its end, it is difficult not to experience a certain perverse aesthetic pleasure mixed with slight nausea because of the ever repeating set of rhetorical and ideological commonplaces in this verse. The war is conceived of in nationalist terms as a conflict between the Germans and the Czechs or Slavs in general and as the cataclysm of Western civilization. These views often intertwine with the notion that the Prague Uprising and the Soviet Liberation of the Bohemian Lands constituted a chiliastic beginning of a new era. The expression of these ideological interpretations often draws on ‘ancient’ anti-German resentment, Czech nationalist mythology, Panslavism, and heavily biblical or liturgical language and imagery. In this essay I will discuss how Czech verse published immediately after the end of the war deals with the experience of the war and its aftermath. In the first part, I look at recurrent mythological motifs and iconography and the role metaphor has in shaping and promoting ideological constructs. In the second part, I look at the portrayal of the war in the work of the poets of Skupina 42 (Group 42) as an alternative to the mythologizing convention of Czech post-war poetry. I focus particularly on Jirhi Kolarh (1914–2002) and his 1945 collection Sedm kantat (Seven cantatas) because it is the only work written by a member of Skupina 42 devoted to the Liberation and the Prague Uprising. In the last two parts of the essay I look at the change in Kolarh’s view of the war and the Uprising in his writing of the late 1940s and early 1950s.

Female Literature of Migration in Italy

Starting symbolically from a place of transit and mobility such as the Galleria in Naples, I look at the pace of immigration movements to Italy from both ex-colonial territories and other countries. Precarity characterizes the migrant condition in Italy: entrance and stay permits; work and housing, which are difficult to obtain and always temporary; bureaucratic control is severe and the right to citizenship is distant. The collective amnesia of the colonial enterprise obscures the fact that at least some of the guests of today were the hosts of yesterday. I analyse these, and other aspects, in the literature of migration that in recent decades has emerged in Italy, focusing on women's writing and confronting the problem of how long it will take for this literature to receive recognition in the Italian literary canon. In women's narratives, precarity emerges in the journey of emigration, described as a real odyssey; in tensions over identity and language; in contrasting cultures of departure and cultures of destination; in the problematic concept of ‘home’. Racial and gender differences subsumed in the colour of skin are a recurrent motif. For women, hardships may be more deeply felt: isolation and loneliness is augmented by the distance from children and family; the relationship between past and present more troublesome as it often leads to a double oppression. independence is more fiercely fought for in the affirmation of identity. Finally, I show that, alongside conditions of isolation and despair, strength and hope in the new life emerge from these writings, touching on the importance of writing in Italian and on the motives leading to this choice.

Nazi Cinema Revisited

As an enduringly popular topic in fi lm history, the study of Nazi cinema now has a history of its own. The “canonical story” of Nazi cinema studies that most of these books rehearse in their introductions runs something like this: in the 1960s and 70s, historians and political scientists initiated the fi eld with a “fi rst wave” of work on Nazi propaganda; this groundwork has been followed, since the mid-1990s, by a new, revisionist historiography informed by methodologies in fi lm and cultural studies, whose focus has been popular genre cinema. The two publications widely recognized as having set off this “second wave” were Linda Schulte-Sasse’s Entertaining the Third Reich (Duke University Press, 1996) and Eric Rentschler’s The Ministry of Illusion (Harvard University Press, 1996). In a clear sign of a disciplinary paradigm shift, these two texts now serve as the established reference points for new work. A decade on, it is time to take stock. Have scholars continued to pursue the directions opened up by the shift from a “fi rst” to a “second” wave historiography? In the ever-accumulating work, what is truly new? Which questions still remain open? The work considered here is diverse and wide-ranging, so I shall confi ne myself to recurrent motifs, common assumptions, and the degree to which individual contributions diverge from the canonical story to offer new vistas. Reviewing these books, one is struck by a recurrent fi gure around which questions of fi lm and popular culture under National Socialism converge: each of these authors has something to tell us about the fi gure of the female fi lm star. The touchstone for most authors remains Zarah Leander, about whose post-war career among queer audiences much has been written (notably by Alice Kuzniar Queer German Cinema [Stanford University Press, 2000]); the contributions here insist on placing the Swedish-born diva—“arguably Nazism’s biggest and most complicated star persona” (Ascheid, 9)—back in her “original” historical contexts, with a particular emphasis on her function as a contradictory cultural icon during the war years, when she starred in the home-front fi lm Die grosse Liebe (The Great Love, 1942). The recurrence of Leander refl ects an implicit scholarly consensus that she best incarnates the ideological functions and limitations of Nazi stardom. Underpinning this consensus, we can infer, fi rst, the methodological conviction that stardom constitutes an epicenter of popular culture, and, second, the more or less explicitly argued assumption that the gender politics of popular culture are signifi ed with particular acuity by the female star. In Hitler’s Heroines, Ascheid programmatically unravels this assumption with the intention of offering “a more complex feminist history of women in the Third Reich” (8). She juxtaposes normative notions of Nazi womanhood with the rather more complex performances and images of femininity on view in the cinema. Drawing on theorizations of stardom in Cultural Studies, Ascheid argues that “the stars of fascism must be seen as containing the cultural incongruities of the period, or better, as the embodiments of particular societal confl icts and contradictions” (35). Viewed through this lens, the Hungarian-born Kristina Soderbaum appears as an unruly incarnation of melodramatic “excess.” Lilian Harvey, whose career spans the Weimar and Nazi years and includes a stint in Hollywood, looks rather more cosmopolitan and “modern” than National Socialist ideals of womanhood would allow; and Zarah Leander, whom the fi lm studios “imported” from Sweden by way of Vienna as a replacement for Marlene Dietrich, becomes an “exemplary fi gure of contradiction and incoherence” (161). While Ascheid occasionally overreaches in her valuation of such contradictions and their potential to destabilize the ideological matrix of National Socialism, these broad arguments are born out in some detail through both textual and contextual readings. A substantial and often stunningly revealing sampling of the trade and popular press adds depth, buttressing Ascheid’s claims. While each of the stars discussed in Hitler’s Heroines is certainly unique, they do represent certain cultural “types” of the kind that were prevalent during the Weimar period (to wit, Harvey’s “girlish” image) and that have been charted in typological star studies from Edgar Morin onward. By contrast, Leni Riefenstahl—if she is to be considered under the

FR3D: finding local and composite recurrent structural motifs in RNA 3D structures

New methods are described for finding recurrent three-dimensional (3D) motifs in RNA atomic-resolution structures. Recurrent RNA 3D motifs are sets of RNA nucleotides with similar spatial arrangements. They can be local or composite. Local motifs comprise nucleotides that occur in the same hairpin or internal loop. Composite motifs comprise nucleotides belonging to three or more different RNA strand segments or molecules. We use a base-centered approach to construct efficient, yet exhaustive search procedures using geometric, symbolic, or mixed representations of RNA structure that we implement in a suite of MATLAB programs, "Find RNA 3D" (FR3D). The first modules of FR3D preprocess structure files to classify base-pair and -stacking interactions. Each base is represented geometrically by the position of its glycosidic nitrogen in 3D space and by the rotation matrix that describes its orientation with respect to a common frame. Base-pairing and base-stacking interactions are calculated from the base geometries and are represented symbolically according to the Leontis/Westhof basepairing classification, extended to include base-stacking. These data are stored and used to organize motif searches. For geometric searches, the user supplies the 3D structure of a query motif which FR3D uses to find and score geometrically similar candidate motifs, without regard to the sequential position of their nucleotides in the RNA chain or the identity of their bases. To score and rank candidate motifs, FR3D calculates a geometric discrepancy by rigidly rotating candidates to align optimally with the query motif and then comparing the relative orientations of the corresponding bases in the query and candidate motifs. Given the growing size of the RNA structure database, it is impossible to explicitly compute the discrepancy for all conceivable candidate motifs, even for motifs with less than ten nucleotides. The screening algorithm that we describe finds all candidate motifs whose geometric discrepancy with respect to the query motif falls below a user-specified cutoff discrepancy. This technique can be applied to RMSD searches. Candidate motifs identified geometrically may be further screened symbolically to identify those that contain particular basepair types or base-stacking arrangements or that conform to sequence continuity or nucleotide identity constraints. Purely symbolic searches for motifs containing user-defined sequence, continuity and interaction constraints have also been implemented. We demonstrate that FR3D finds all occurrences, both local and composite and with nucleotide substitutions, of sarcin/ricin and kink-turn motifs in the 23S and 5S ribosomal RNA 3D structures of the H. marismortui 50S ribosomal subunit and assigns the lowest discrepancy scores to bona fide examples of these motifs. The search algorithms have been optimized for speed to allow users to search the non-redundant RNA 3D structure database on a personal computer in a matter of minutes.

Across One Sixth of the World: Dziga Vertov, Travel Cinema, and Soviet Patriotism

The films of Dziga Vertov display a persistent fascination with travel. Movement across vast spaces is perhaps the most recurrent motif in his oeuvre, and the cine-race [kino-probeg] a genre developed by Vertov's group of filmmakers, the Kinoks l stands as an encompassing metaphor for Vertov's own work. His cinematographic journeys transported viewers to the most remote as well as to the most advanced sites of the Soviet universe, creating a heterogeneous cine-world stretching from the desert to the icy tundra and featuring customs, costumes, and cultural practices unfamiliar to most of his audience. Vertov's personal travelogue began when he moved from his native Bialystok2 in the ex-Pale of Settlement to Petrograd and later to Moscow, from where, having embarked on a career in filmmaking, he proceeded to the numerous sites of the Civil War. Recalling his first steps in cinema, Vertov described a complex itinerary that included Rostov, Chuguev, the Lugansk suburbs, and even the Astrakhan steppes.3 In the early 1920s, when the film distribution network was severely restricted by the Civil War and uneven nationalization, traveling and filmmaking were inseparable. Along with other filmmakers, he used an improvised