Occurrence and Function of Hoogsteen Base Pairs in Nucleic Acids

Nucleic acids (DNA and RNA) play essential roles in the central dogma of biology for the storage and transfer of genetic information. The unique chemical and conformational structures of nucleic acids – the double helix composed of complementary Watson-Crick base pairs, provide the structural basis to carry out their biological functions. DNA double helix can dynamically accommodate Watson-Crick and Hoogsteen base-pairing, in which the purine base is flipped by ~180° degrees to adopt syn rather than anti conformation as in Watson-Crick base pairs. There is growing evidence that Hoogsteen base pairs play important roles in DNA replication, recognition, damage or mispair accommodation and repair. Here, we constructed a database for existing Hoogsteen base pairs in DNA duplexes by a structure-based survey from the Protein Data Bank, and structural analyses based on the resulted Hoogsteen structures revealed that Hoogsteen base pairs occur in a wide variety of biological contexts and can induce DNA kinking towards the major groove. As there were documented difficulties in modeling Hoogsteen or Watson-Crick by crystallography, we collaborated with the Richardsons’ lab and identified potential Hoogsteen base pairs that were mis-modeled as Watson-Crick base pairs which suggested that Hoogsteen can be more prevalent than it was thought to be. We developed solution NMR method combined with the site-specific isotope labeling to characterize the formation of, or conformational exchange with Hoogsteen base pairs in large DNA-protein complexes under solution conditions, in the absence of the crystal packing force. We showed that there are enhanced chemical exchange, potentially between Watson-Crick and Hoogsteen, at a sharp kink site in the complex formed by DNA and the Integration Host Factor protein. In stark contrast to B-form DNA, we found that Hoogsteen base pairs are strongly disfavored in A-form RNA duplex. Chemical modifications N1-methyl adenosine and N1-methyl guanosine that block Watson-Crick base-pairing, can be absorbed as Hoogsteen base pairs in DNA, but rather potently destabilized A-form RNA and caused helix melting. The intrinsic instability of Hoogsteen base pairs in A-form RNA endows the N1-methylation as a functioning post-transcriptional modification that was known to facilitate RNA folding, translation and potentially play roles in the epitranscriptome. On the other hand, the dynamic property of DNA that can accommodate Hoogsteen base pairs could be critical to maintaining the genome stability.

Pollen record of sediment core GeoB1008-3 from the Congo fan

Palynological investigation of the marine core, GeoB1008-3, from near the mouth of the Congo river (6°35.6'S/10°19.1'E), provides information about the changes in vegetation and climate in West Equatorial Africa during the last 190 ka. The pollen diagram is divided into zones 1-6 which are considered to correspond in time with the marine isotope stages 1-6. Oscillations in temperature and moisture are indicated during the cold stage 6. During stage 5, two cooler periods (5d and 5b) can be shown with an expansion of Podocarpus forests to lower elevations on the expense of lowland rain forest. Extended mangrove swamps existed along the coast in times of high sea level (stages 5 and 1).

Lower Albian benthic foraminifera

The Early Albian Oceanic Anoxic Event 1b (OAE 1b) black shale is interrupted by one or more ventilation events that display significant changes in benthic and planktic populations. Within the OAE 1b sections studied, at ODP Site 1049, DSDP Site 545, and the Vocontian Basin, the benthic foraminiferal repopulation events last between ~500 and ~1,250 years and occur with a cyclicity of approximately 5.7 kyr. This period may represent an amplitude modulation of the precessional cycle. The OAE 1b sections from the marginal setting of the Vocontian Basin exhibit up to eight repopulation events. In contrast, there is only one repopulation event identified in the Atlantic OAE 1b sections from the Mazagan Plateau (DSDP 545) and Blake Nose (ODP 1049). Within the margin of dating uncertainties, this supraregional repopulation event occurred synchronously in the Vocontian Basin and the Atlantic Ocean. While the OAE 1b black shale formed under extremely warm and humid conditions, the repopulation events occurred during intervals of short-term cooling and reduced humidity at deep-water formation sites. The resulting increase in evaporation led to enhanced formation of low-latitude deep water, thus improving the ventilation of the sea floor.

Pollen analysis of sediment profile WO1 from Wollingster See

A palynological study of a 15 m sediment core from the centre of Lake Wollingst (water depth 14,5 m) is presented. The pollen record shows 3 lateglacial thermomers, called Meiendorf, Bölling, Alleröd and the early holocene Friesland-Thermomer. The succession of forest vegetation taking place on the lake surroundings during the Holocene was typical for older moraine soils which are poor in nutrients: forest vegetation started with birch and pine, followed by hazel, oak and elm in the Boreal and by alder, lime and ash-tree in the Atlantic. Beech and hornbeam reached the area during Subboreal. However, due to the poor soils they spread out only after the Iron Age. With the deforestation during the medieval time the lake lost its character of a primeval forest lake. Lake Wollingst was oligotrophic since its origin at the end of the Pleniglacial. After medieval forest-clearing the lake has changed its quality of water particularly in connection with hemp- and flax-rotting. The modem sediments in this profile are completely disturbed. They contain reworked material, a lot of blue-green algae and remains of Bosmina longirostris indicating eutrophic conditions.

Structural evolution of the Lesser Himalayan fold-thrust belt of west central Nepal

The Lesser Himalayan fold-thrust belt on the south flank of the Jajarkot klippe in west central Nepal was mapped in detail between the Main Central thrust in the north and the Main Boundary thrust in the south. South of the Jajarkot klippe, the fold-thrust belt involves sandstone, shale and carbonate rocks that are unmetamorphosed in the foreland and increase in metamorphic grade with higher structural position to sub-greenschist facies towards the hinterland. The exposed stratigraphy is correlative with the Proterozoic Ranimata, Sangram, Galyang, Syangia Formations and Lakharpata Group of Western Nepal and overlain by the Paleozoic Tansen and Kali Gandaki Groups. Based on field mapping and cross-section construction, three distinct thrust sheets were identified separated by top-to-the-south thrust faults. From the foreland (south) to the hinterland (north), the first thrust sheet in the immediate hanging wall of the Main Boundary thrust defines an open syncline. The second thrust sheet contains a very broad synformal duplex, which is structurally stacked against the third thrust sheet containing a homoclinal panel of the oldest exposed Proterozoic stratigraphy. Outcrop scale folds throughout the study area are predominantly south vergent, open, and asymmetric reflecting the larger regional scale folding style, which corroborate the top-to-the-south deformation style seen in the faults of the region. Field techniques were complemented with microstructural and quartz crystallographic c-axis preferred orientation analyses using a petrographic microscope and a fabric analyzer, respectively. Microstructural analysis identified abundant strain-induced recrystallization textures and occasional occurrences of top-to-the-south shear-sense indicators primarily in the hinterland rocks in the immediate footwall of the Main Central Thrust. Top-to-the-south shearing is also supported by quartz crystallographic c-axis preferred orientations. Quartz recrystallization textures indicate an increase in deformation temperature towards the Main Central thrust. A line balance estimate indicates that approximately 15 km of crustal shortening was accommodated by folding and faulting in the fold-thrust belt south of the Jajarkot klippe. Additionally, estimations of shortening velocity suggest that the shortening velocity operating in this section of the fold-thrust belt between 23 to 14 Ma was slower than what is currently observed as a result of the ongoing deformation of the Sub-Himalayan fold-thrust belt.

Design and Synthesis of Acridine-Based Macrocyclic G-Quadruplex DNA Ligands

DNA sequences that are rich in the guanine nucleic base possess the ability to fold into higher order structures called G-quadruplexes. These higher level structures are formed as a result of two sets of four guanine bases hydrogen-bonding together in a planar arrangement called a guanine quartet. Guanine quartets subsequently stack upon each other to form quadruplexes. G-quadruplexes are mainly localized in telomeres as well as in oncogene promoters. One unique and promising therapeutic approach against cancer involves targeting and stabilizing G-quadruplexes with small molecules, generally in order to suppress oncogene expression and telomerase enzyme activity; the latter has been found to contribute to “out-of control” cell growth in ca. 80-85% of all cancer cells and primary tumours while being absent in normal somatic cells. In this work, we present efforts towards designing and synthesizing acridine-based macrocycles (Mh) and (Mb) with the purpose of providing potential G4 ligands that are suited for selective binding to G4 vs. duplex DNA, and stabilize G-quadruplex structures. Two ligands described in this study include an acridine core which provides an aromatic surface capable of π-π interactions with the surface of G-quadruplexes. The successful synthesis of 4,5-diaminoacridine is described in chapter 2, as an essential fragment of the macrocycles (Mh) and (Mb). In order to investigate the synthetic method for macrocyclization, model compounds composing almost half of the designed macrocycles were explored. As discussed in chapter 3, the synthesis of the model compound for (Mb) turned out to be challenging. However, as a step towards the synthesis of (Mh), the synthesis of the hydrogen-containing model compound, which is almost half of the desired macrocycle (Mh) was achieved in our group and proved to be promising.

Rate Maximization of Decode-and-Forward Relaying Systems with RF Energy Harvesting

We consider a three-node decode-and-forward (DF) half-duplex relaying system, where the source first harvests RF energy from the relay, and then uses this energy to transmit information to the destination via the relay. We assume that the information transfer and wireless power transfer phases alternate over time in the same frequency band, and their time fraction (TF) may change or be fixed from one transmission epoch (fading state) to the next. For this system, we maximize the achievable average data rate. Thereby, we propose two schemes: (1) jointly optimal power and TF allocation, and (2) optimal power allocation with fixed TF. Due to the small amounts of harvested power at the source, the two schemes achieve similar information rates, but yield significant performance gains compared to a benchmark system with fixed power and fixed TF allocation.

Beam division multiple access for massive MIMO downlink transmission

We study a multiuser multicarrier downlink communication system in which the base station (BS) employs a large number of antennas. By assuming frequency-division duplex operation, we provide a beam domain channel model as the number of BS antennas grows asymptotically large. With this model, we first derive a closed-form upper bound on the achievable ergodic sum-rate before developing necessary conditions to asymptotically maximize the upper bound, with only statistical channel state information at the BS. Inspired by these conditions, we propose a beam division multiple access (BDMA) transmission scheme, where the BS communicates with users via different beams. For BDMA transmission, we design user scheduling to select users within non-overlapping beams, work out an optimal pilot design under a minimum mean square error criterion, and provide optimal pilot sequences by utilizing the Zadoff-Chu sequences. The proposed BDMA scheme reduces significantly the pilot overhead, as well as, the processing complexity at transceivers. Simulations demonstrate the high spectral efficiency of BDMA transmission and the advantages in the bit error rate performance of the proposed pilot sequences.

Efeitos da simpaticotomia endoscópica sobre as artérias carótidas e vertebrais na terapêutica cirúrgica da hiperidrose primária

Analisar, em pacientes submetidos a simpaticotomia videotoracoscópica para tratamento da Hiperidrose Primária (HP), as conseqüências hemodinâmicas da desnervação vascular das artérias carótidas e vertebrais após a trans-secção cirúrgica da cadeia simpática torácica (simpaticotomia), através da mensuração de parâmetros ultra-sonográficos. Método: Vinte e quatro pacientes portadores de HP submetidos a quarenta e oito simpaticotomias torácicas endoscópicas foram avaliados através da mensuração da velocidade de pico sistólico (VPS), velocidade de pico diastólico (VPD), índice de pulsatibilidade (IP) e índice de resistência (IR) nas artérias carótidas comuns, internas e externas, além da artéria vertebral bilateralmente usando o eco-doppler duplex scan. As avaliações foram realizadas antes da intervenção cirúrgica e trinta dias após o procedimento. O teste de Wilcoxon foi usado na análise das diferenças entre as variáveis antes e depois da simpaticotomia. Resultados: A simpaticotomia no nível de T3 foi a trans-secção mais realizada (95,83%), seja isoladamente (25%) ou associada a T4 (62,50%) ou a T2 (8,33%). Houve aumento significativo no IR e no IP da artéria carótida comum bilateralmente (p<0,05). A VPD da artéria carótida interna diminuiu em ambos os lados (p<0,05). A VPS e a VPD da artéria vertebral direita também aumentaram (p<0,05). Achados assimétricos foram observados, de modo que artérias do lado direito foram as mais freqüentemente afetadas. Conclusões: Alterações hemodinâmicas foram observadas nas artérias vertebral e carótida após simpaticotomia para tratamento de HP. VPS foi o parâmetro mais freqüentemente alterado, principalmente nas artérias do lado direito, representando alterações assimétricas significantes nas artérias carótida e vertebral. Entretanto, são necessárias pesquisas subseqüentes para verificar se essas alterações são definitivas ou temporárias, uma vez que as inferências clínicas somente terão validação se as alterações forem permanentes

RECQ5 promotes recombination and mutagenesis at targeted nicks through disruption of RAD51 filaments

Thesis (Ph.D.)--University of Washington, 2016-08

Influence of grinding operations on surface integrity and chloride induced stress corrosion cracking of stainless steels

Stainless steels were developed in the early 20th century and are used where both the mechanical properties of steels and corrosion resistance are required. There is continuous research to allow stainless steel components to be produced in a more economical way and be used in more harsh environments. A necessary component in this effort is to correlate the service performance with the production processes. The central theme of this thesis is the mechanical grinding process.  This is commonly used for producing stainless steel components, and results in varied surface properties that will strongly affect their service life. The influence of grinding parameters including abrasive grit size, machine power and grinding lubricant were studied for 304L austenitic stainless steel (Paper II) and 2304 duplex stainless steel (Paper I). Surface integrity was proved to vary significantly with different grinding parameters. Abrasive grit size was found to have the largest influence. Surface defects (deep grooves, smearing, adhesive/cold welding chips and indentations), a highly deformed surface layer up to a few microns in thickness and the generation of high level tensile residual stresses in the surface layer along the grinding direction were observed as the main types of damage when grinding stainless steels. A large degree of residual stress anisotropy is interpreted as being due to mechanical effects dominating over thermal effects. The effect of grinding on stress corrosion cracking behaviour of 304L austenitic stainless steel in a chloride environment was also investigated (Paper III). Depending on the surface conditions, the actual loading by four-point bend was found to deviate from the calculated value using the formula according to ASTM G39 by different amounts. Grinding-induced surface tensile residual stress was suggested as the main factor to cause micro-cracks initiation on the ground surfaces. Grinding along the loading direction was proved to increase the susceptibility to chloride-induced SCC, while grinding perpendicular to the loading direction improved SCC resistance. The knowledge obtained from this work can provide a reference for choosing appropriate grinding parameters when fabricating stainless steel components; and can also be used to help understanding the failure mechanism of ground stainless steel components during service.

Ulnar artery aneurysm: case report and review of the literature

Aim. We report a case of ulnar and palmar arch artery aneurysm in a 77 years old man without history of any occupational or recreational trauma, vasculitis, infections or congenital anatomic abnormalities. We also performed a computed search of literature in PUBMED using the keywords “ulnar artery aneurysm” and “palmar arch aneurysm”. Case report. A 77 years old male patient was admitted to hospital with a pulsing mass at distal right ulnar artery and deep palmar arch; at ultrasound and CT examination a saccular aneurysm of 35 millimeters at right ulnar artery and a 15 millimeters dilatation at deep palmar arch were detected. He was asymptomatic for distal embolization and pain. In local anesthesia ulnar artery and deep palmar arch dilatations were resected. Reconstruction of vessels was performed through an end-to-end microvascular repair. Histological examination confirmed the absence of vasculitis and collagenopaties. In postoperative period there were no clinical signs of peripheral ischemia, Allen’s test and ultrasound examination were normal. At follow-up of six months, the patient was still asymptomatic with a normal Allen test, no signs of distal digital ischemia and patency of treated vessel with normal flow at duplex ultrasound. Conclusion. True spontaneous aneurysms of ulnar artery and palmar arch are rare and can be successfully treated with resection and microvascular reconstruction.

Radio over fiber enabling PON fronthaul in a two-tiered cloud

Avec l’avènement des objets connectés, la bande passante nécessaire dépasse la capacité des interconnections électriques et interface sans fils dans les réseaux d’accès mais aussi dans les réseaux coeurs. Des systèmes photoniques haute capacité situés dans les réseaux d’accès utilisant la technologie radio sur fibre systèmes ont été proposés comme solution dans les réseaux sans fil de 5e générations. Afin de maximiser l’utilisation des ressources des serveurs et des ressources réseau, le cloud computing et des services de stockage sont en cours de déploiement. De cette manière, les ressources centralisées pourraient être diffusées de façon dynamique comme l’utilisateur final le souhaite. Chaque échange nécessitant une synchronisation entre le serveur et son infrastructure, une couche physique optique permet au cloud de supporter la virtualisation des réseaux et de les définir de façon logicielle. Les amplificateurs à semi-conducteurs réflectifs (RSOA) sont une technologie clé au niveau des ONU(unité de communications optiques) dans les réseaux d’accès passif (PON) à fibres. Nous examinons ici la possibilité d’utiliser un RSOA et la technologie radio sur fibre pour transporter des signaux sans fil ainsi qu’un signal numérique sur un PON. La radio sur fibres peut être facilement réalisée grâce à l’insensibilité a la longueur d’onde du RSOA. Le choix de la longueur d’onde pour la couche physique est cependant choisi dans les couches 2/3 du modèle OSI. Les interactions entre la couche physique et la commutation de réseaux peuvent être faites par l’ajout d’un contrôleur SDN pour inclure des gestionnaires de couches optiques. La virtualisation réseau pourrait ainsi bénéficier d’une couche optique flexible grâce des ressources réseau dynamique et adaptée. Dans ce mémoire, nous étudions un système disposant d’une couche physique optique basé sur un RSOA. Celle-ci nous permet de façon simultanée un envoi de signaux sans fil et le transport de signaux numérique au format modulation tout ou rien (OOK) dans un système WDM(multiplexage en longueur d’onde)-PON. Le RSOA a été caractérisé pour montrer sa capacité à gérer une plage dynamique élevée du signal sans fil analogique. Ensuite, les signaux RF et IF du système de fibres sont comparés avec ses avantages et ses inconvénients. Finalement, nous réalisons de façon expérimentale une liaison point à point WDM utilisant la transmission en duplex intégral d’un signal wifi analogique ainsi qu’un signal descendant au format OOK. En introduisant deux mélangeurs RF dans la liaison montante, nous avons résolu le problème d’incompatibilité avec le système sans fil basé sur le TDD (multiplexage en temps duplexé).