Understanding mutational and selective processes that govern gene duplication in mammals

Abstract : Gene duplication is an essential source of material for the origin of genetic novelties. The reverse transcription of source gene mRNA followed by the genomic insertion of the resulting cDNA - retroposition - has provided the human genome with at least ~3600 detectable retrocopies. We find that ~30% of these retrocopies are transcribed, generally in testes. Their transcription often relies on preexisting regulatory elements (or open chromatin) close to their insertion site, which is illustrated by mRNA molecules containing retrocopies fused to their neighboring genes. Retrocopies appear to have been profoundly shaped by selection. Consistently, human retrocopies with an intact open reading (ORF) are more often transcribed than retropseudogenes, which leads to a minimal estimate of 120 functional retrogenes present in our genome. We also performed an analysis of Ka/Ks for human retrocopies. This analysis demonstrates that several intact retrocopies evolved under purifying selection and yields an estimated formation rate of ~1 retrogene per million year in the primate lineage. Using DNA sequencing and evolutionary simulations, we have identified 7 such primate-specific retrogenes that emerged on the lineage leading to humans In therian genomes, we found an excess of retrogenes with X-linked parents. Expression analyses support the idea that this "out of X" movement was driven by natural selection to produce autosomal functional counterparts for X-linked genes, which are silenced during male meiosis. Phylogenetic dating of this "out of X" movement suggests that our sex chromosomes arose about 180 MYA ago and are thus much younger than previously thought. Finally, we have also analyzed young gene duplications (and deletions) that arose by non allelic-homologous recombination and are not fixed in species. Using wild-caught and laboratory animals, we detected thousands of DNA segments that are polymorphic in copy number in mice. These copy number variants were found to profoundly alter the transcriptome of several mouse tissues. Strikingly, their influence on gene expression is not limited to the gene they contain but seems to extend to genes located up to 1.5 million bases away.

Ancient protostome origin of chemosensory ionotropic glutamate receptors and the evolution of insect taste and olfaction.

Ionotropic glutamate receptors (iGluRs) are a highly conserved family of ligand-gated ion channels present in animals, plants, and bacteria, which are best characterized for their roles in synaptic communication in vertebrate nervous systems. A variant subfamily of iGluRs, the Ionotropic Receptors (IRs), was recently identified as a new class of olfactory receptors in the fruit fly, Drosophila melanogaster, hinting at a broader function of this ion channel family in detection of environmental, as well as intercellular, chemical signals. Here, we investigate the origin and evolution of IRs by comprehensive evolutionary genomics and in situ expression analysis. In marked contrast to the insect-specific Odorant Receptor family, we show that IRs are expressed in olfactory organs across Protostomia--a major branch of the animal kingdom that encompasses arthropods, nematodes, and molluscs--indicating that they represent an ancestral protostome chemosensory receptor family. Two subfamilies of IRs are distinguished: conserved "antennal IRs," which likely define the first olfactory receptor family of insects, and species-specific "divergent IRs," which are expressed in peripheral and internal gustatory neurons, implicating this family in taste and food assessment. Comparative analysis of drosophilid IRs reveals the selective forces that have shaped the repertoires in flies with distinct chemosensory preferences. Examination of IR gene structure and genomic distribution suggests both non-allelic homologous recombination and retroposition contributed to the expansion of this multigene family. Together, these findings lay a foundation for functional analysis of these receptors in both neurobiological and evolutionary studies. Furthermore, this work identifies novel targets for manipulating chemosensory-driven behaviours of agricultural pests and disease vectors.

Control of gene expression in melanocytes and RPE by conserved distal regulatory elements

Résumé Durant le développement embryonnaire, les cellules pigmentaires des mammifères se développent à partir de deux origines différentes : les melanocytes se développent à partir de la crête neurale alors que les cellules de la rétine pigmentaire (RP) ont une origine neuronale. Un grand nombre de gènes sont impliqués dans la pigmentation dont les gènes de la famille tyrosinase à savoir Tyr, Tyrp1 et Dct. Certaines études ont suggéré que les gènes de la pigmentation sont régulés de manière différentielle dans les mélanocytes et dans la RP. Dans ce travail, les gènes de la famille tyrosinase ont été étudiés comme modèle de la régulation des gènes de la pigmentation par des éléments régulateurs agissant à distance. II a été montré que le promoteur du gène Tyrp1pouvait induire l'expression d'un transgène uniquement dans la RP alors que ce gène est aussi exprimé dans les mélanocytes comme le montre le phénotype des souris mutantes pour Tyrp1. Ce résultat suggère que les éléments régulateurs du promoteur sont suffisants pour l'expression dans la RP mais pas pour l'expression dans les mélanocytes. J'ai donc cherché à identifier la séquence qui régule l'expression dans les mélanocytes. Un chromosome artificiel bactérien (CAB) contenant le gène Tyrp1 s'est avéré suffisant pour induire l'expression dans les mélanocytes, comme démontré par la correction du phénotype mutant. La séquence de ce CAB contient plusieurs régions très conservées qui pourraient représenter de nouveaux éléments régulateurs. Par la suite, j'ai focalisé mon analyse sur une séquence située à -I5 kb qui s'est révélée être un amplificateur spécifique aux mélanocytes comme démontré par des expériences de cultures cellulaire et de transgenèse. De plus, une analyse poussée de cet élément a révélé que le facteur de transcription Sox 10 représentait un transactivateur de cet amplificateur. Comme pour Tyrp1, la régulation du gène tyrosinase est contrôlée par différents éléments régulateurs dans les mélanocytes et la RP. Il a été montré que le promoteur de tyrosinase n'était pas suffisant pour une forte expression dans les mélanocytes et la RP. De plus, l'analyse de la région située en amont a révélé la présence d'un amplificateur nécessaire à l'expression dans les mélanocytes à la position -15 kb. Cet amplificateur n'est toutefois pas actif dans la RP mais agit comme un répresseur dans ces cellules. Ces résultats indiquent que certains éléments nécessaires à l'expression dans les deux types de cellules pigmentaires sont absents de ces constructions. Comme pour Tyrp1, j'ai en premier lieu démontré qu'un CAB était capable de corriger le phénotype albinique, puis ai inséré un gène reporter (lacZ) dans le CAB par recombinaison homologue et ai finalement analysé l'expression du reporter en transgenèse. Ces souris ont montré une expression forte du lacZ dans les mélanocytes et la RP, ce qui indique que le CAB contient les séquences régulatrices nécessaires à l'expression correcte de tyrosinase. Afin de localiser plus précisément les éléments régulateurs, j'ai ensuite généré des délétions dans le CAB et analysé l'expression du lacZ en transgenèse. La comparaison de séquences génomiques provenant de différentes espèces a permis par la suite d'identifier des régions représentant de nouveaux éléments régulateurs potentiels. En utilisant cette approche, j'ai identifié une région qui se comporte comme un amplificateur dans la RP et qui est nécessaire à l'expression de tyrosinase dans ce tissu. De plus, j'ai identifié les facteurs de transcription Mitf et Sox10 comme transactivateurs de l'amplificateur spécifique aux mélanocytes situé à -15 kb. L'identification et la caractérisation des ces éléments régulateurs des gènes tyrosinase et Tyrp1confirme donc que la régulation différentielle des gènes dans les mélanocytes et la RP est liée à des éléments régulateurs séparés. Summary Pigment cells of mammals originate from two different lineages: melanocytes arise from the neural crest, whereas cells of the retinal pigment epithelium (RPE) originate from the optic cup of the developing forebrain. A large set of genes are involved in pigmentation, including the members of the tyrosinase gene family, namely tyrosinase, Tyrp1 and Dct. Previous studies have suggested that pigmentation genes are differentially regulated in melanocytes and RPE. In this work, the tyrosinase gene family was used as a model for studying the involvement of distal regulatory elements in pigment cell-specific gene expression. The promoter of the Tyrp1 gene has been shown to drive detectable transgene expression only to the RPE, even though the gene is also expressed in melanocytes as evident from Tyrp1-mutant mice. This indicates that the regulatory elements responsible for Tyrp1 gene expression in the RPE are not sufficient for expression in melanocytes. I thus searched for a putative melanocyte-specific regulatory sequence and demonstrate that a bacterial artificial chromosome (BAC) containing the Tyrp1 gene and surrounding sequences is able to target transgenic expression to melanocytes and to rescue the Tyrp1 b (brown) phenotype. This BAC contains several highly conserved non-coding sequences that might represent novel regulatory elements. I further focused on a sequence located at -15 kb which I identified as amelanocyte-specific enhancer as shown by cell culture and transgenic mice. In addition, further functional analysis identified the transcription factor Sox10 as being able to bind and transactivate this enhancer. As for Tyrp1, tyrosinase gene regulation is mediated by different cis-regulatory elements in melanocytes and RPE. It was shown that the tyrosinase promoter was not sufficient to confer strong and specific expression in melanocytes and RPE. Moreover, analysis of tyrosinase upstream sequence, revealed the presence of a specific enhancer at position -15 kb which was necessary to confer strong expression in melanocytes. This enhancer element however failed to act as an enhancer in the RPE, but rather repressed expression. This indicates that some regulatory elements required for tyrosinase expression in both RPE and melanocytes are still missing from these constructs. As for Tyrp1, I first demonstrated that a BAC containing the Tyr gene is able to rescue the Tyr c (albino) phenotype in mice, then I inserted a lacZ reporter gene in the BAC by homologous recombination, and finally analysed the pattern of lacZ expression in transgenic mice. These mice showed strong lacZ expression in both RPE and melanocytes, indicating that the BAC contains the regulatory sequences required for proper tyrosinase expression. In order to localize more precisely these regulatory elements, I have then generated several deletions in the BAC and analysed lacZ expression in transgenic mice. Multi-species comparative genomic analysis then allowed identifying conserved sequences that potentially represent novel regulatory elements. Using this experimental approach, I identified a region that behaves as a RPE-specific enhancer and that is required for tyrosinase expression in the retina] pigment epithelium. In addition, I identified the transcription factors Mitf and Sox l0 as being transactivators of the melanocyte-specific enhancer located at -l5 kb. The identification and characterization of these tyrosinase and Tyrp1 distal regulatory element supports the idea that separate regulatory sequences mediate differential gene expression in melanocytes and RPE.

Fabrication and characterization of silicon position sensitive particle detectors

Position sensitive particle detectors are needed in high energy physics research. This thesis describes the development of fabrication processes and characterization techniques of silicon microstrip detectors used in the work for searching elementary particles in the European center for nuclear research, CERN. The detectors give an electrical signal along the particles trajectory after a collision in the particle accelerator. The trajectories give information about the nature of the particle in the struggle to reveal the structure of the matter and the universe. Detectors made of semiconductors have a better position resolution than conventional wire chamber detectors. Silicon semiconductor is overwhelmingly used as a detector material because of its cheapness and standard usage in integrated circuit industry. After a short spread sheet analysis of the basic building block of radiation detectors, the pn junction, the operation of a silicon radiation detector is discussed in general. The microstrip detector is then introduced and the detailed structure of a double-sided ac-coupled strip detector revealed. The fabrication aspects of strip detectors are discussedstarting from the process development and general principles ending up to the description of the double-sided ac-coupled strip detector process. Recombination and generation lifetime measurements in radiation detectors are discussed shortly. The results of electrical tests, ie. measuring the leakage currents and bias resistors, are displayed. The beam test setups and the results, the signal to noise ratio and the position accuracy, are then described. It was found out in earlier research that a heavy irradiation changes the properties of radiation detectors dramatically. A scanning electron microscope method was developed to measure the electric potential and field inside irradiated detectorsto see how a high radiation fluence changes them. The method and the most important results are discussed shortly.

Sex-chromosome evolution of Palearctic tree frogs in space and time

Sexual reproduction is nearly universal in eukaryotes and genetic determination of sex prevails among animals. The astonishing diversity of sex-determining systems and sex chromosomes is yet bewildering. Some taxonomic groups possess conserved and dimorphic sex chromosomes, involving a functional copy (e.g. mammals' X, birds' Z) and a degenerated copy (mammals' Y, birds' W), implying that sex- chromosomes are expected to decay. In contrast, others like amphibians, reptiles and fishes yet maintained undifferentiated sex chromosomes. Why such different evolutionary trajectories? In this thesis, we empirically test and characterize the main hypotheses proposed to prevent the genetic decay of sex chromosomes, namely occasional X-Y recombination and frequent sex-chromosome transitions, using the Palearctic radiation of Hyla tree frogs as a model system. We take a phylogeographic and phylogenetic approach to relate sex-chromosome recombination, differentiation, and transitions in a spatial and temporal framework. By reconstructing the recent evolutionary history of the widespread European tree frog H. arborea, we showed that sex chromosomes can recombine in males, preventing their differentiation, a situation that potentially evolves rapidly. At the scale of the entire radiation, X-Y recombination combines with frequent transitions to prevent sex-chromosome degeneration in Hyla: we traced several turnovers of sex-determining system within the last 10My. These rapid changes seem less random than usually assumed: we gathered evidences that one chromosome pair is a sex expert, carrying genes with key role in animal sex determination, and which probably specialized through frequent reuse as a sex chromosome in Hyla and other amphibians. Finally, we took advantage of secondary contact zones between closely-related Hyla lineages to evaluate the consequences of sex chromosome homomorphy on the genetics of speciation. In comparison with other systems, the evolution of sex chromosomes in Hyla emphasized the existence of consistent evolutionary patterns within the chaotic diversity of flexibility of cold-blooded vertebrates' sex-determining systems, and provides insights into the evolution of recombination. Beyond sex-chromosome evolution, this work also significantly contributed to speciation, phylogeography and applied conservation research. -- La reproduction sexuée est quasi-universelle chez les eucaryotes et le sexe est le plus souvent déterminé génétiquement au sein du règne animal. L'incroyable diversité des systèmes de reproduction et des chromosomes sexuels est particulièrement étonnante. Certains groupes taxonomiques possèdent des chromosomes sexuels dimorphiques et très conservés, avec une copie entièrement fonctionnelle (ex : le X des mammifères, le Z des oiseaux) et une copie dégénérée (ex : le Y des mammifères, le W des oiseaux), suggérant que les chromosomes sexuels sont voués à se détériorer. Cependant les chromosomes sexuels d'autres groupes tels que les amphibiens, les reptiles et les poissons sont pour la plupart indifférenciés. Comment expliquer des trajectoires évolutives si différentes? Au cours de cette thèse, nous avons étudié empiriquement les processus évolutifs pouvant maintenir les chromosomes sexuels intacts, à savoir la recombinaison X-Y occasionnel ainsi que les substitutions fréquentes de chromosomes sexuels, en utilisant les rainettes Paléarctiques du genre Hyla comme modèle d'étude. Nous avons adopté une approche phylogéographique et phylogénétique pour appréhender les événements de recombinaison, de différenciation et de transitions de chromosomes sexuels dans un contexte spatio-temporel. En retraçant l'histoire évolutive récente de la rainette verte H. arborea, nous avons mis en évidence que les chromosomes sexuels pouvaient recombiner chez les mâles, empêchant ainsi leur différenciation, et que ce processus avait le potentiel d'évoluer très rapidement. A l'échelle plus globale de la radiation, il apparait que les phénomènes de recombinaison X-Y soient également accompagnés de substitutions de chromosomes sexuels, et participent de concert au maintien de chromosomes sexuels intacts dans les populations: le système de détermination du sexe des rainettes a changé plusieurs fois au cours des 10 derniers millions d'années. Ces transitions fréquentes ne semblent pas aléatoires: nous avons identifié une paire de chromosomes qui présente des caractéristiques présageant d'une spécialisation dans le déterminisme du sexe (notamment car elle possède des gènes importants pour cette fonction), et qui a été réutilisée plusieurs fois comme tel chez les rainettes ainsi que d'autres amphibiens. Enfin, nous avons étudié l'hybridation entre différentes espèces dans leurs zones de contact, afin d'évaluer si l'absence de différenciation entre X et Y jouaient un rôle dans les processus génétiques de spéciation. Outre son intérêt pour la compréhension de l'évolution des chromosomes sexuels, ce travail contribue de manière significative à d'autres domaines de recherche tels que la spéciation, la phylogéographie, ainsi que la biologie de la conservation.

The eukaryotic Pso2/Snm1/Artemis proteins and their function as genomic and cellular caretakers

DNA double-strand breaks (DSBs) represent a major threat to the genomic stability of eukaryotic cells. DNA repair mechanisms such as non-homologous end joining (NHEJ) are responsible for the maintenance of eukaryotic genomes. Dysfunction of one or more of the many protein complexes that function in NHEJ can lead to sensitivity to DNA damaging agents, apoptosis, genomic instability, and severe combined immunodeficiency. One protein, Pso2p, was shown to participate in the repair of DSBs induced by DNA inter-strand cross-linking (ICL) agents such as cisplatin, nitrogen mustard or photo-activated bi-functional psoralens. The molecular function of Pso2p in DNA repair is unknown, but yeast and mammalian cell line mutants for PSO2 show the same cellular responses as strains with defects in NHEJ, e.g., sensitivity to ICLs and apoptosis. The Pso2p human homologue Artemis participates in V(D)J recombination. Mutations in Artemis induce a variety of immunological deficiencies, a predisposition to lymphomas, and an increase in chromosomal aberrations. In order to better understand the role of Pso2p in the repair of DSBs generated as repair intermediates of ICLs, an in silico approach was used to characterize the catalytic domain of Pso2p, which led to identification of novel Pso2p homologues in other organisms. Moreover, we found the catalytic core of Pso2p fused to different domains. In plants, a specific ATP-dependent DNA ligase I contains the catalytic core of Pso2p, constituting a new DNA ligase family, which was named LIG6. The possible functions of Pso2p/Artemis/Lig6p in NHEJ and V(D)J recombination and in other cellular metabolic reactions are discussed.

Comparative electron impact and fast atom bombardment mass spectrometric studies of some HMPA adducts of phenyltin and phenyllead halides and studies of strong hydrogen bonding by FAB-MS

The fragmentation patterns and mass spectra of some phenyl tin and -lead halide adducts with hexamethylphosphoramide are compared by subjecting them t~ electron impact and fast atom bombardment ionization in a mass spectrometer. This comparison is restricted to the metal-containing ions. Ligand-exchange mechanisms of some of the metal-containing species are explored by FAB-MS. Several moisturesensitive organo-metallics and H-bonded systems have been examined by FAB for attempted characterization, but without any success. Scavenging and trapping of water molecules by complex aggregates in solutions of quaternary ammonium fluorides and hydroxides are investigated by FAB to complement previous NMR-studies.

Solute effects on the production and decay of primary species in the flash photolysis of indole

Maximum production rates ofs and decay kinetics for the hydrated electron, the indolyl neutral radical and the indole triplet state have been obtained in the microsecond, broadband (X > 260 nm) flash photolysis of helium-saturated, neutral aqueous solutions of indole, in the absence and in the presence of the solutes NaBr, BaCl2*2H20 and CdSCV Fluorescence spectra and fluorescence lifetimes have also been obtained in the absence and in the presence of the above solutes, The hydrated electron is produced monophotonically and biphotonically at an apparent maximum rate which is increased by BaCl2*2H20 and decreased by NaBr and CdSOif. The neutral indolyl radical may be produced monophotonically and biphotonically or strictly monophotonically at an apparent maximum rate which is increased by NaBr and CdSO^ and is unaffected by BaCl2*2H20. The indole triplet state is produced monophotonically at a maximum rate which is increased by all solutes. The hydrated electron decays by pseudo first order processes, the neutral indolyl radical decays by second order recombination and the indole triplet state decays by combined first and second order processes. Hydrated electrons are shown to react with H , H2O, indole, Na and Cd"*""1"". No evidence has been found for the reaction of hydrated electrons with Ba . The specific rate of second order neutral indolyl radical recombination is unaffected by NaBr and BaCl2*2H20, and is increased by CdSO^. Specific rates for both first and second order triplet state decay processes are increased by all solutes. While NaBr greatly reduced the fluorescence lifetime and emission band intensity, BaCl2*2H20 and CdSO^ had no effect on these parameters. It is suggested that in solute-free solutions and in those containing BaCl2*2H20 and CdSO^, direct excitation occurs to CTTS states as well as to first excited singlet states. It is further suggested that in solutions containing NaBr, direct excitation to first excited singlet states predominates. This difference serves to explain increased indole triplet state production (by ISC from CTTS states) and unchanged fluorescence lifetimes and emission band intensities in the presence of BaCl2*2H20 and CdSOt^., and increased indole triplet state production (by ISC from S^ states) and decreased fluorescence lifetime and emission band intensity in the presence of NaBr. Evidence is presented for (a) very rapid (tx ^ 1 us) processes involving reactions of the hydrated electron with Na and Cd which compete with the reformation of indole by hydrated electron-indole radical cation recombination, and (b) first and second order indole triplet decay processes involving the conversion of first excited triplet states to vibrationally excited ground singlet states.

Letter to S.D. Woodruff from William Colburn with the letterhead “Office of Detroit Bridge and Iron Works”

Letter to S.D. Woodruff from William Colburn with the letterhead “Office of Detroit Bridge and Iron Works” regarding stating that he closed up the business with Dewey’s. He states that “we” now have “warranty deeds” from them for exclusive rights for all time for hunting, shooting and trapping, Mar. 20, 1884.

Investigations on Photoconductivity and Electrical Switiching in Selected Chalcogenide Glasses

In this thesis, we present the results of our investigations on the photoconducting and electrical switching properties of selected chalcogenide glass systems. We have used XRD and X-ray photoelectron spectroscopy (XPS) analysis for confinuing the amorphous nature of these materials and for confirming their constituents respectively.Photoconductivity is the enhancement in electrical conductivity of materials brought about by the motion of charge carriers excited by absorbed radiation. The phenomenon involves absorption, photogeneration, recombination and transport processes and it gives good insight into the density of states in the energy gap of solids due to the presence of impurities and lattice defects. Photoconductivity measurements lead to the determination of such important parameters as quantum efficiency, photosensiti\'ity, spectral sensitivity and carrier lifetime. Extensive research work on photoconducting properties of amorphous semiconductors has resulted in the development of a variety of very sensitive photodetectors. Photoconductors are finding newer and newer uses eyery day. CdS, CdSe. Sb2S3, Se, ZnO etc, are typical photoconducting materials which are used in devices like vidicons, light amplifiers, xerography equipment etc.Electrical switching is another interesting and important property possessed by several Te based chalcogenides. Switching is the rapid and reversible transition between a highly resistive OFF state, driven by an external electric field and characterized by a threshold voltage, and a low resistivity ON state, Switching can be either threshold type or memory type. The phenomenon of switching could find applications in areas like infonnation storage, electrical power control etc. Investigations on electrical switching in chalcogenide glasses help in understanding the mechanism of switching which is necessary to select and modify materials for specific switching applications.Analysis of XRD pattern gives no further infonuation about amorphous materials than revealing their disordered structure whereas x-ray photoelectron spectroscopy,XPS) provides information about the different constituents present in the material. Also it gives binding energies (b.e.) of an element in different compounds and hence b.e. shift from the elemental form.Our investigations have been concentrated on the bulk glasses, Ge-In-Se, Ge-Bi-Se and As-Sb-Se for photoconductivity measurements and In-Te for electrical switching. The photoconducting properties of Ge-Sb-Se thin films prepared by sputtering technique have also been studied. The bulk glasses for the present investigations are prepared by the melt quenching technique and are annealed for half an hour at temperatures just below their respective glass transition temperatures. The dependence of photoconducting propenies on composition and temperature are investigated in each system. The electrical switching characteristics of In-Te system are also studied with different compositions and by varying the temperature.

Polarization and correlation phenomena in the radiative electron capture by bare highly-charged ions

In dieser Arbeit wird die Wechselwirkung zwischen einem Photon und einem Elektron im starken Coulombfeld eines Atomkerns am Beispiel des radiativen Elektroneneinfangs beim Stoß hochgeladener Teilchen untersucht. In den letzten Jahren wurde dieser Ladungsaustauschprozess insbesondere für relativistische Ion–Atom–Stöße sowohl experimentell als auch theoretisch ausführlich erforscht. In Zentrum standen dabei haupsächlich die totalen und differentiellen Wirkungsquerschnitte. In neuerer Zeit werden vermehrt Spin– und Polarisationseffekte sowie Korrelationseffekte bei diesen Stoßprozessen diskutiert. Man erwartet, dass diese sehr empfindlich auf relativistische Effekte im Stoß reagieren und man deshalb eine hervorragende Methode zu deren Bestimmung erhält. Darüber hinaus könnten diese Messungen auch indirekt dazu führen, dass man die Polarisation des Ionenstrahls bestimmen kann. Damit würden sich neue experimentelle Möglichkeiten sowohl in der Atom– als auch der Kernphysik ergeben. In dieser Dissertation werden zunächst diese ersten Untersuchungen zu den Spin–, Polarisations– und Korrelationseffekten systematisch zusammengefasst. Die Dichtematrixtheorie liefert hierzu die geeignete Methode. Mit dieser Methode werden dann die allgemeinen Gleichungen für die Zweistufen–Rekombination hergeleitet. In diesem Prozess wird ein Elektron zunächst radiativ in einen angeregten Zustand eingefangen, der dann im zweiten Schritt unter Emission des zweiten (charakteristischen) Photons in den Grundzustand übergeht. Diese Gleichungen können natürlich auf beliebige Mehrstufen– sowie Einstufen–Prozesse erweitert werden. Im direkten Elektroneneinfang in den Grundzustand wurde die ”lineare” Polarisation der Rekombinationsphotonen untersucht. Es wurde gezeigt, dass man damit eine Möglichkeit zur Bestimmung der Polarisation der Teilchen im Eingangskanal des Schwerionenstoßes hat. Rechnungen zur Rekombination bei nackten U92+ Projektilen zeigen z. B., dass die Spinpolarisation der einfallenden Elektronen zu einer Drehung der linearen Polarisation der emittierten Photonen aus der Streuebene heraus führt. Diese Polarisationdrehung kann mit neu entwickelten orts– und polarisationsempfindlichen Festkörperdetektoren gemessen werden. Damit erhält man eine Methode zur Messung der Polarisation der einfallenden Elektronen und des Ionenstrahls. Die K–Schalen–Rekombination ist ein einfaches Beispiel eines Ein–Stufen–Prozesses. Das am besten bekannte Beispiel der Zwei–Stufen–Rekombination ist der Elektroneneinfang in den 2p3/2–Zustand des nackten Ions und anschließendem Lyman–1–Zerfall (2p3/2 ! 1s1/2). Im Rahmen der Dichte–Matrix–Theorie wurden sowohl die Winkelverteilung als auch die lineare Polarisation der charakteristischen Photonen untersucht. Beide (messbaren) Größen werden beträchtlich durch die Interferenz des E1–Kanals (elektrischer Dipol) mit dem viel schwächeren M2–Kanal (magnetischer Quadrupol) beeinflusst. Für die Winkelverteilung des Lyman–1 Zerfalls im Wasserstoff–ähnlichen Uran führt diese E1–M2–Mischung zu einem 30%–Effekt. Die Berücksichtigung dieser Interferenz behebt die bisher vorhandene Diskrepanz von Theorie und Experiment beim Alignment des 2p3/2–Zustands. Neben diesen Ein–Teichen–Querschnitten (Messung des Einfangphotons oder des charakteristischen Photons) wurde auch die Korrelation zwischen den beiden berechnet. Diese Korrelationen sollten in X–X–Koinzidenz–Messungen beobbachtbar sein. Der Schwerpunkt dieser Untersuchungen lag bei der Photon–Photon–Winkelkorrelation, die experimentell am einfachsten zu messen ist. In dieser Arbeit wurden ausführliche Berechnungen der koinzidenten X–X–Winkelverteilungen beim Elektroneneinfang in den 2p3/2–Zustand des nackten Uranions und beim anschließenden Lyman–1–Übergang durchgeführt. Wie bereits erwähnt, hängt die Winkelverteilung des charakteristischen Photons nicht nur vom Winkel des Rekombinationsphotons, sondern auch stark von der Spin–Polarisation der einfallenden Teilchen ab. Damit eröffnet sich eine zweite Möglichkeit zur Messung der Polaristion des einfallenden Ionenstrahls bzw. der einfallenden Elektronen.

Origin and evolution of 3'UTR of flaviviruses: long direct repeats as a basis for the formation of secondary structures and their significance for virus transmission

The 3' untranslated regions (3'UTRs) of flaviviruses are reviewed and analyzed in relation to short sequences conserved as direct repeats (DRs). Previously, alignments of the 3'UTRs have been constructed for three of the four recognized flavivirus groups, namely mosquito-borne, tick-borne, and nonclassified flaviviruses (MBFV, TBFV, and NCFV, respectively). This revealed (1) six long repeat sequences (LRSs) in the 3'UTR and open-reading frame (ORF) of the TBFV, (2) duplication of the 3'UTR of the NCFV by intramolecular recombination, and (3) the possibility of a common origin for all DRs within the MBFV. We have now extended this analysis and review it in the context of all previous published analyses. This has been achieved by constructing a robust alignment between all flaviviruses using the published DRs and secondary RNA structures as "anchors" to reveal additional homologies along the 3'UTR. This approach identified nucleotide regions within the MBFV, NKV (no-known vector viruses), and NCFV 3'UTRs that are homologous to different LRSs in the TBFV 3'UTR and ORF. The analysis revealed that some of the DRs and secondary RNA structures described individually within each flavivirus group share common evolutionary origins. The 3'UTR of flaviviruses, and possibly the ORF, therefore probably evolved through multiple duplication of an RNA domain, homologous to the LRS previously identified only in the TBFV. The short DRs in all virus groups appear to represent the evolutionary remnants of these domains rather than resulting from new duplications. The relevance of these flavivirus DRs to evolution, diversity, 3'UTR enhancer function, and virus transmission is reviewed.

Knowledge, attitudes and practices of farmers on rodent pests and their management in the lowlands of the Sierra Madre Biodiversity Corridor, Philippines

A survey of the knowledge, attitudes and practices (KAP) of 100 rice farmers and 50 coconut farmers was conducted in the coastal lowland agro-ecosystems of the Sierra Madre Biodiversity Corridor, Luzon, Philippines to identify current rodent management practices and to understand the extent of rat damage and the attitudes of farmers to community actions for rodent management. Pests were most commonly listed as one of the three most important rice and coconut production constraints. Other major crop production constraints were typhoons and insufficient water. Farmers consider rats to be the major pest of coconut and of rice during the wet season rice crop, with average yield losses of 3.0% and 13.2%, respectively. Rice and coconut farmers practised a wide range of rodent management techniques. These included scrub clearance, hunting and trapping. Of the 42 rice farmers and 3 coconut farmers that applied rodenticides to control rodents, all used the acute rodenticide, zinc phosphide. However, only ten rice farmers (23.8%) applied rodenticides prior to the booting stage and only seven farmers (15.6%) conducted pre-baiting before applying zinc phosphide. The majority of farmers belonged to farmer organisations and believed that rat control can only be done by farmers working together. However, during the last cropping season, less than a third of rice farmers (31.2%) applied rodent management as a group. In order to reduce the impact of rodents on the farmers of the coastal lowlands of the Sierra Madre Biodiversity Corridor, integrated management strategies need to be developed that specifically target the pest rodents in a sustainable manner, and community actions for rodent management should be promoted.

An eight-parent multiparent advanced generation inter-cross population for winter-sown wheat: creation, properties, and validation

MAGIC populations represent one of a new generation of crop genetic mapping resources combining high genetic recombination and diversity. We describe the creation and validation of an eight-parent MAGIC population consisting of 1091 F7 lines of winter-sown wheat (Triticum aestivum L.). Analyses based on genotypes from a 90,000-single nucleotide polymorphism (SNP) array find the population to be well-suited as a platform for fine-mapping quantitative trait loci (QTL) and gene isolation. Patterns of linkage disequilibrium (LD) show the population to be highly recombined; genetic marker diversity among the founders was 74% of that captured in a larger set of 64 wheat varieties, and 54% of SNPs segregating among the 64 lines also segregated among the eight founder lines. In contrast, a commonly used reference bi-parental population had only 54% of the diversity of the 64 varieties with 27% of SNPs segregating. We demonstrate the potential of this MAGIC resource by identifying a highly diagnostic marker for the morphological character "awn presence/absence" and independently validate it in an association-mapping panel. These analyses show this large, diverse, and highly recombined MAGIC population to be a powerful resource for the genetic dissection of target traits in wheat, and it is well-placed to efficiently exploit ongoing advances in phenomics and genomics. Genetic marker and trait data, together with instructions for access to seed, are available at http://www.niab.com/MAGIC/.

Search for Genomic Alterations in Monozygotic Twins Discordant for Cleft Lip and/or Palate

Phenotypically discordant monozygotic twins offer the possibility of gene discovery through delineation of molecular abnormalities in one member of the twin pair. One proposed mechanism of discordance is postzygotically occurring genomic alterations resulting from mitotic recombination and other somatic changes. Detection of altered genomic fragments can reveal candidate gene loci that can be verified through additional analyses. We investigated this hypothesis using array comparative genomic hybridization; the 50K and 250K Affymetrix GeneChip (R) SNP arrays and an Illumina custom array consisting of 1,536 SNPs, to scan for genomic alterations in a sample of monozygotic twin pairs with discordant cleft lip and/or palate phenotypes. Paired analysis for deletions, amplifications and loss of heterozygosity, along with sequence verification of SNPs with discordant genotype calls did not reveal any genomic discordance between twin pairs in lymphocyte DNA samples. Our results demonstrate that postzygotic genomic alterations are not a common cause of monozygotic twin discordance for isolated cleft lip and/or palate. However, rare or balanced genomic alterations, tissue-specific events and small aberrations beyond the detection level of our experimental approach cannot be ruled out. The stability of genomes we observed in our study samples also suggests that detection of discordant events in other monozygotic twin pairs would be remarkable and of potential disease significance.