Period determination in the food-entrainable and methamphetamine-sensitive circadian oscillator(s)

Daily rhythmic processes are coordinated by circadian clocks, which are present in numerous central and peripheral tissues. In mammals, two circadian clocks, the food-entrainable oscillator (FEO) and methamphetamine-sensitive circadian oscillator (MASCO), are "black box" mysteries because their anatomical loci are unknown and their outputs are not expressed under normal physiological conditions. In the current study, the investigation of the timekeeping mechanisms of the FEO and MASCO in mice with disruption of all three paralogs of the canonical clock gene, Period, revealed unique and convergent findings. We found that both the MASCO and FEO in Per1(-/-)/Per2(-/-)/Per3(-/-) mice are circadian oscillators with unusually short (similar to 21 h) periods. These data demonstrate that the canonical Period genes are involved in period determination in the FEO and MASCO, and computational modeling supports the hypothesis that the FEO and MASCO use the same timekeeping mechanism or are the same circadian oscillator. Finally, these studies identify Per1(-/-)/Per2(-/-)/Per3(-/-) mice as a unique tool critical to the search for the elusive anatomical location(s) of the FEO and MASCO.

A Dark Matter Search with AMANDA : Limits on the Muon Flux from Neutralino Annihilations at the Centre of the Earth with 1997-99 Data

The nature of the dark matter in the Universe is one of the greatest mysteries in modern astronomy. The neutralino is a nonbaryonic dark matter candidate in minimal supersymmetric extensions to the standard model of particle physics. If the dark matter halo of our galaxy is made up of neutralinos some would become gravitationally trapped inside massive bodies like the Earth. Their pair-wise annihilation produces neutrinos that can be detected by neutrino experiments looking in the direction of the centre of the Earth. The AMANDA neutrino telescope, currently the largest in the world, consists of an array of light detectors buried deep in the Antarctic glacier at the geographical South Pole. The extremely transparent ice acts as a Cherenkov medium for muons passing the array and using the timing information of detected photons it is possible to reconstruct the muon direction. A search has been performed for nearly vertically upgoing neutrino induced muons with AMANDA-B10 data taken over the three year period 1997-99. No excess above the atmospheric neutrino background expectation was found. Upper limits at the 90 % confidence level has been set on the annihilation rate of neutralinos at the centre of the Earth and on the muon flux induced by neutrinos created by the annihilation products.

La figure de Méduse. Réécritures ovidiennes entre XVIe et XVIIe siècle

Starting from an original assumption that Ovid is one of the most influential and studied European mythographers from ancient times till at least the end of the XVII century, my research is about rediscovering Medusa's myth which has been brought to us from Metamorphosis during the period of time between the mid XVI and the last years of the XVII century. The main thread that leads the research trough English, French, Spanish and Italian Literatures gets particularly clarified in the crucial crux that binds the image of Gorgon, the protector of hight mysteries, tightly correlated to the goddess of knowledge, Minerva, and the attraction/dismay for knowing so far considered inaccessible but now perceived as possible (so more attractive than before) thanks to the scientific and geographic discoveries of the Renaissance.

Statistical mechanics of protein complexed and condensed DNA

In this thesis I treat various biophysical questions arising in the context of complexed / ”protein-packed” DNA and DNA in confined geometries (like in viruses or toroidal DNA condensates). Using diverse theoretical methods I consider the statistical mechanics as well as the dynamics of DNA under these conditions. In the first part of the thesis (chapter 2) I derive for the first time the single molecule ”equation of state”, i.e. the force-extension relation of a looped DNA (Eq. 2.94) by using the path integral formalism. Generalizing these results I show that the presence of elastic substructures like loops or deflections caused by anchoring boundary conditions (e.g. at the AFM tip or the mica substrate) gives rise to a significant renormalization of the apparent persistence length as extracted from single molecule experiments (Eqs. 2.39 and 2.98). As I show the experimentally observed apparent persistence length reduction by a factor of 10 or more is naturally explained by this theory. In chapter 3 I theoretically consider the thermal motion of nucleosomes along a DNA template. After an extensive analysis of available experimental data and theoretical modelling of two possible mechanisms I conclude that the ”corkscrew-motion” mechanism most consistently explains this biologically important process. In chapter 4 I demonstrate that DNA-spools (architectures in which DNA circumferentially winds on a cylindrical surface, or onto itself) show a remarkable ”kinetic inertness” that protects them from tension-induced disruption on experimentally and biologically relevant timescales (cf. Fig. 4.1 and Eq. 4.18). I show that the underlying model establishes a connection between the seemingly unrelated and previously unexplained force peaks in single molecule nucleosome and DNA-toroid stretching experiments. Finally in chapter 5 I show that toroidally confined DNA (found in viruses, DNAcondensates or sperm chromatin) undergoes a transition to a twisted, highly entangled state provided that the aspect ratio of the underlying torus crosses a certain critical value (cf. Eq. 5.6 and the phase diagram in Fig. 5.4). The presented mechanism could rationalize several experimental mysteries, ranging from entangled and supercoiled toroids released from virus capsids to the unexpectedly short cholesteric pitch in the (toroidaly wound) sperm chromatin. I propose that the ”topological encapsulation” resulting from our model may have some practical implications for the gene-therapeutic DNA delivery process.

Die Bedeutung von molekularem Sauerstoff für die Evolution des genetischen Codes

Die Entstehung und Evolution des genetischen Codes, der die Nukleotidsequenz der mRNA in die Aminosäuresequenz der Proteine übersetzt, zählen zu den größten Rätseln der Biologie. Die ersten Organismen, die vor etwa 3,8 Milliarden Jahren auf der Erde auftraten, nutzten einen ursprünglichen genetischen Code, der vermutlich ausschließlich abiotisch verfügbare Aminosäuren terrestrischer oder extraterrestrischer Herkunft umfasste. Neue Aminosäuren wurden sukzessive biosynthetisiert und selektiv in den Code aufgenommen, welcher in der modernen Form aus bis zu 22 Aminosäuren besteht. Die Ursachen für die Selektion und die Chronologie ihrer Aufnahme sind bis heute unbekannt und sollten im Rahmen der vorliegenden Arbeit erforscht werden. Auf Grundlage quanten-chemischer Berechnungen konnte in dieser Arbeit zunächst ein Zusammenhang zwischen der HOMO-LUMO-Energiedifferenz (H-L-Distanz), die ein inverses quanten-chemisches Korrelat für allgemeine chemische Reaktivität darstellt, und der chronologischen Aufnahme der Aminosäuren in den genetischen Code aufgezeigt werden. Demnach sind ursprüngliche Aminosäuren durch große H-L-Distanzen und neue Aminosäuren durch kleine H-L-Distanzen gekennzeichnet. Bei einer Analyse des Metabolismus von Tyrosin und Tryptophan, bei denen es sich um die beiden jüngsten Standard-Aminosäuren handelt, wurde ihre Bedeutung als Vorläufer von Strukturen ersichtlich, die sich durch eine hohe Redox-Aktivität auszeichnen und deren Synthese gleichzeitig molekularen Sauerstoff erfordert. Aus diesem Grund wurden die Redox-Aktivitäten der 20 Standard-Aminosäuren gegenüber Peroxylradikalen und weiteren Radikalen getestet. Die Untersuchungen ergaben eine Korrelation zwischen evolutionärem Auftreten und chemischer Reaktivität der jeweiligen Aminosäure, die sich insbesondere in der effizienten Reaktion zwischen Tryptophan bzw. Tyrosin und Peroxylradikalen widerspiegelte. Dies indizierte eine potentielle Bedeutung reaktiver Sauerstoffspezies (ROS) bei der Konstituierung des genetischen Codes. Signifikante Mengen an ROS wurden erst zu Beginn der Oxygenierung der Geobiosphäre, die als Great Oxidation Event (GOE) bezeichnet wird und vor circa 2,3 Milliarden Jahren begann, gebildet und müssen zur oxidativen Schädigung vulnerabler, zellulärer Strukturen geführt haben. Aus diesem Grund wurde das antioxidative Potential von Aminosäuren beim Prozess der Lipidperoxidation untersucht. Es konnte gezeigt werden, dass lipophile Derivate von Tryptophan und Tyrosin befähigt sind, die Peroxidation von Rattenhirnmembranen zu verhindern und humane Fibroblasten vor oxidativem Zelltod zu schützen. Daraus gründete sich das in dieser Arbeit aufgestellte Postulat eines Selektionsvorteils primordialer Organismen während des GOEs, die Tryptophan und Tyrosin als redox-aktive Aminosäuren in Membranproteine einbauen konnten und somit vor Oxidationsprozessen geschützt waren. Demzufolge wurde die biochemische Reaktivität als Selektionsparameter sowie oxidativer Stress als prägender Faktor der Evolution des genetischen Codes identifiziert.

Untersuchung der Ladung des Neutrons

Die Quantisierung der elektrischen Ladung ist eine der größten Fragestellungen der Physik, die bis heute nicht verstanden ist. Im Standardmodell der Teilchenphysik ist sie beispielsweise nicht mathematisch inhärent erklärbar. Dadurch wäre es möglich, dass das Neutron eine winzige Ladung tragen kann. In dieser Arbeit wurde eine Apparatur auf Grundlage eines Vorgängerexperiments entwickelt, mit der eine Untersuchung der Ladung des Neutrons mit höchster Präzision durchgeführt werden kann. Dabei werden ultrakalte Neutronen in einem optischen System einem elektrischen Feld zwischen zwei Elektrodenplatten ausgesetzt. In der ersten Ladungsmessung mit dieser Apparatur konnte eine statistische Sensitivität von δq≈2,4∙10⁻²⁰ e/√d erreicht werden. Diese Sensitivität ist die höchste, die bisher mit ultrakalten Neutronen für eine Ladungsmessung erreicht werden konnte. In dieser Arbeit wurde das Konzept des Vorgängerexperiments grundlegend überarbeitet, um die Sensitivität der Apparatur zu erhöhen. Es wurden detaillierte Untersuchungen der Systematik der Apparatur durchgeführt und das theoretische Potential der Sensitivität von derzeit δq≈10⁻²¹ e/√d ermittelt. Mit dieser Apparatur wurde der Grundstein für die Messung einer neuen niedrigeren oberen Grenze der elektrischen Ladung des Neutrons gelegt. In nächster Zeit kann dadurch eine niedrigere obere Grenze für die Ladung des Neutrons von q≈10⁻²² e erzielt werden.

Representations of the Human/ Nonhuman Primate Divide: the Influence of Science, Fiction, and Science-Fiction on the Concept of 'Being Human'

For as far back as human history can be traced, mankind has questioned what it means to be human. One of the most common approaches throughout Western culture's intellectual tradition in attempts to answering this question has been to compare humans with or against other animals. I argue that it was not until Charles Darwin's publication of The Descent of Man and Selection in Relation to Sex (1871) that Western culture was forced to seriously consider human identity in relation to the human/ nonhuman primate line. Since no thinker prior to Charles Darwin had caused such an identity crisis in Western thought, this interdisciplinary analysis of the history of how the human/ nonhuman primate line has been understood focuses on the reciprocal relationship of popular culture and scientific representations from 1871 to the Human Genome Consortium in 2000. Focusing on the concept coined as the "Darwin-Müller debate," representations of the human/ nonhuman primate line are traced through themes of language, intelligence, and claims of variation throughout the popular texts: Descent of Man, The Jungle Books (1894), Tarzan of the Apes (1914), and Planet of the Apes (1963). Additional themes such as the nature versus nurture debate and other comparative phenotypic attributes commonly used for comparison between man and apes are also analyzed. Such popular culture representations are compared with related or influential scientific research during the respective time period of each text to shed light on the reciprocal nature of Western intellectual tradition, popular notions of the human/ nonhuman primate line, and the development of the field of primatology. Ultimately this thesis shows that the Darwin-Müller debate is indeterminable, and such a lack of resolution makes man uncomfortable. Man's unsettled response and desire for self-knowledge further facilitates a continued search for answers to human identity. As the Human Genome Project has led to the rise of new debates, and primate research has become less anthropocentric over time, the mysteries of man's future have become more concerning than the questions of our past. The human/ nonhuman primate line is reduced to a 1% difference, and new debates have begun to overshadow the Darwin-Müller debate. In conclusion, I argue that human identity is best represented through the metaphor of evolution: both have an unknown beginning, both have an indeterminable future with no definite end, and like a species under the influence of evolution, what it means to be human is a constant, indeterminable process of change.

"Brethren upon the same level" : membership and class in Calumet's Masonic Lodge

The Keweenaw Peninsula of Upper Michigan was a ethnic conglomerate of cultures and ideas, with people attracted to the area by the mineral wealth found along the Copper Range. The center of copper mining from the mid 1860s to 1968 was in the vicinity of Calumet Township, home to the world-famous Calumet and Hecla Mining Company. The township depended on the mines and the company’s president Agassiz’s strove to make the area a “model community,” that included groups such as the Free and Accepted Masons. Men from myriad backgrounds arrived in Calumet from the British Isles, Germany, Finland, Eastern and Southern Europe and the Eastern United States. As in other communities from the time period these men formed common interest groups like Masonic Lodge 271, which received its charter in 1870. Gentlemen joined with merchants and craftsmen. They became “brethren upon the same level,” and were elevated to the status of Master Mason. This symbolic transformation within the Lodge removed the men from the “profane world” outside the sanctity of Masonry, and in the ritualistic transformation of the meeting they were reborn into Masonry’s sacred mysteries. Masonry acted as a means of moral guidance to men and gave them access to a larger social and economic community through a common connection of brotherhood. As the candidates moved through the three Blue Lodge degrees of Entered Apprentice, Fellowcraft, and Master Mason they saw each other as “brethren upon the same level” – all economic classes equal within the Masonic Lodge. To examine equality within Lodge 271, this study sorted workers into classes to allow a comparison of Lodge 271’s membership. Possibly a comparison between other lodges can be drawn from the membership. The Union Building in Calumet, MI will be examined for its role in the ritualistic transformation of Masonry as it housed Masonic activities and transformations. This transformation brought men into the lodge of brothers. While Masonry professed equality between members however, to what extent did the membership of the lodge reflect this between the brethren? To what extent did economic class determine who was made “brethren upon the same level? 1 Arthur Thurner, Calumet Copper and People: History of a Michigan Mining Community, 1864-1970 (Hancock, MI: Book Concern, 1974), 122.

TB research at UT-Houston--a review of cord factor: new approaches to drugs, vaccines and the pathogenesis of tuberculosis.

Tuberculosis remains a major threat as drug resistance continues to increase. Pulmonary tuberculosis in adults is responsible for 80% of clinical cases and nearly 100% of transmission of infection. Unfortunately, since we have no animal models of adult type pulmonary tuberculosis, the most important type of disease remains largely out of reach of modern science and many fundamental questions remain unanswered. This paper reviews research dating back to the 1950's providing compelling evidence that cord factor (trehalose 6,6 dimycolate [TDM]) is essential for understanding tuberculosis. However, the original papers by Bloch and Noll were too far ahead of their time to have immediate impact. We can now recognize that the physical and biologic properties of cord factor are unprecedented in science, especially its ability to switch between two sets of biologic activities with changes in conformation. While TDM remains on organisms, it protects them from killing within macrophages, reduces antibiotic effectiveness and inhibits the stimulation of protective immune responses. If it comes off organisms and associates with lipid, TDM becomes a driver of tissue damage and necrosis. Studies emanating from cord factor research have produced (1) a rationale for improving vaccines, (2) an approach to new drugs that overcome natural resistance to antibiotics, (3) models of caseating granulomas that reproduce multiple manifestations of human tuberculosis. (4) evidence that TDM is a key T cell antigen in destructive lesions of tuberculosis, and (5) a new understanding of the pathology and pathogenesis of postprimary tuberculosis that can guide more informative studies of long standing mysteries of tuberculosis.

Review of Clément Vidal, "The Beginning and the End. The Meaning of Life in a Cosmological Perspective"

No more ground control. Dissertations ideally always have been ambitious, and this one can’t claim to be too humble in these regards. Together the pieces of this work form a world view that the author confesses to finding ‘magnificent’. The story he tells is one in which intelligence and complexity are keys to unlock the universe’s mysteries. Vidal tackles questions like ‘What is philosophy?’, ‘Where does it all come from?’, Where are we going?’, ‘Are we alone in the universe?’ and even ‘What is good and what is evil?’. Questions which philosophers for ages have tried to answer.

Path characteristics and colony arrival-departure statistics of king penguins (Aptenodytes patagonicus) on Possession and Kerguelen Island

Orientation based on visual cues can be extremely difficult in crowded bird colonies due to the presence of many individuals. We studied king penguins (Aptenodytes patagonicus) that live in dense colonies and are constantly faced with such problems. Our aims were to describe adult penguin homing paths on land and to test whether visual cues are important for their orientation in the colony. We also tested the hypothesis that older penguins should be better able to cope with limited visual cues due to their greater experience. We collected and examined GPS paths of homing penguins. In addition, we analyzed 8 months of penguin arrivals to and departures from the colony using data from an automatic identification system. We found that birds rearing chicks did not minimize their traveling time on land and did not proceed to their young (located in creches) along straight paths. Moreover, breeding birds' arrivals and departures were affected by the time of day and luminosity levels. Our data suggest that king penguins prefer to move in and out of the colony when visual cues are available. Still, they are capable of navigating even in complete darkness, and this ability seems to develop over the years, with older breeding birds more likely to move through the colony at nighttime luminosity levels. This study is the first step in unveiling the mysteries of king penguin orientation on land.

Los "ejemplares raros" de Botánica del caos de Ana María Shuan

El acercamiento crítico a “Botánica del caos" de Ana María Shua se decide, fundamentalmente, desde el análisis de su paratexto en el que, siguiendo a Genette, se pone de manifiesto la dimensión pragmática de la obra, su relación con el lector. Se intenta dar a conocer la función de algunos de los elementos constitutivos en particular y en relación con el todo integrado. Los ingredientes del paratexto se disponen a la manera de cajas chinas y contienen misterios secretos desplegados en diferentes planos y dimensiones. Las conexiones del entramado perfecto de la estructura de la obra revelan una consideración minuciosa por parte de la autora que demuestra su oficio de acuerdo con los rasgos característicos del género que practica: el microrrelato.

Les mysteres de l'onomastique dans l'Helene d'Euripide

En su Helena, Eurípides teoriza las dificultades de la onomástica: los nombres recubren la identidad de múltiples homónimos o bien un nombre designa muchas esencias de un mismo individuo, como ocurre con la verdadera reina de Esparta y su eídolo. Estas observaciones adquieren una significación teatral, pues un personaje como Teucro, mal integrado en la acción si se tratara del famoso arquero homérico, se insertaría en un rol muy pertinente si se reconociera en él al meteco que denuncia la parodia de los misterios de Eleusis por Alcibíades. Además, cierta tradición crítica ha distinguido trazos del joven estratega bajo la puesta en escena de la protagonista. La obra de Eurípides sugiere, de hecho, de manera esotérica, el progreso escénico de una rehabilitación y de una iniciación no solo de Helena (sobre el plano de la representación mitológica), sino también de Alcibíades (sobre el plano político). Por otra parte, el nombre y la función dramática de Teónoe están realmente demasiado cercanos a aquellos de Téano (la sacerdotisa de Eleusis citada por Plutarco como la única en haberse negado a maldecir a Alcibíades), como para que la similitud onomástica sea fortuita.

Orfeo y Eleusis

Orfeo aparece en múltiples fuentes como fundador de las teletai, esto es, del tipo de ritos a los que pertenecen claramente los Eleusinios, y como autor de poesía religiosa relacionada con ellos. Sin embargo, nadie a´Çü rma que los Misterios Eleusinos sean "ór´Çücos". Por otra parte, varias fuentes consideran a Eumolpo el fundador de los ritos. El artículo trata de explicar esta contradicción. Para ello se examinan los testimonios que relacionan a Orfeo con Eleusis o las teletai en general y los restos de la poesía ór´Çü ca sobre Deméter y Perséfone. Puede concluirse que había dos puntos de vista que coexistían sin solaparse: desde el punto de vista Eleusinio, Eumolpo aparece destacado y los Eumólpidas tienen el privilegio exclusivo de ser hierofantes. Desde el punto de vista ateniense, el prestigio de Orfeo es más "internacional" y sirve mucho mejor sus intereses políticos.